# 2001 Mk4 Jetta Auto (01m) to Manual (02j) swap notes



## SRB94 (Mar 10, 2009)

OK, I fixed my ailing 01M automatic problems on my 2001 VR6 by swaping to the manual 5-speed. The posts by Alphasenior, nosborn94, coolAirVw, swozniac4201, boertje, and many others on this and other forums were a fantastic help, and without them I would probably not have attempted the project at all. Unfortunately the down side of so much information is that it was difficult to keep things straight at times. In any case, thanks to everyone. It is running great now under the Automatic ECU and with the CEL on. The TCU still installed, but everything appears to be working as I had expected. If you don’t need to have the CEL off it is possible to stop here. 

Now it is time to give back a little. My hope with this post is that someday I may be able to help by making it easier to discriminate between the Diesel and the Gasoline swap, as well as the differences between a full conversion and one where you were going to run under the Automatic ECU. Yeah, I know, maybe it’s being picky, but it would have made life easier for me and it was what I spent most of my time on. On the other hand it made for lots of interesting reading. 

Anyway, here are a few things that I thought would be helpful to speed up the next person’s conversion and hopefully avoid some problems. I’m still looking at doing a full conversion by swapping the ECU for a manual unit, but that is in the future.

*Essential Elements*:
1.	Swap trans and shifter per other threads.
2.	Install Clutch pedal and support bracket.
3.	Rewire 175 relay socket for 53 relay to provide clutch/starter interlock and backup lights.
4.	Connect backup light switch.
5.	Cut Yellow/Blue wire at the ECU that is also in the harness being modified under the dash and used for the backup lights.
The details are more than covered elsewhere multiple times and, reading others experiences are of value to understand your vehicle’s differences and possible workarounds. Any additional wiring changes seem to be only required if you are going for a full conversion and installing a manual ECU. Otherwise you have a functioning conversion at this point and it is really not that difficult.

*Wiring*: Be sure to check the wiring diagram for your vehicle. 
1.	What I observed is that the wire colors are generally (but not always) correct in the other posts. Please use caution. 
2.	The terminal numbers for the under dash wiring were correct for me, and probably will be for you, but knowing the numbers made things easy to trace on the diagram so check to be sure. See comments below.
3.	ECU wiring is different between automatic and manual, gasoline and diesel. Some terminals are assigned differently on the ECU.
4.	The diesel ECU’s can be recoded to manual, the Gasoline cannot.
5.	Check into your Immobilizer level before you commit to making ECU swaps. Past 2001 it appears to become more difficult to make a complete conversion. Read http://wiki.ross-tech.com/wiki/index.php/Immobilizer for more details.
6.	I left the TCU (transmission control unit) in place and connected. When I disconnected it the ASR light came on. ASR appears to be working with it plugged in.
7.	There is some throttle flair on shifts. This may be a programming difference in the response of the Auto ECU as compared to the manual ECU.
8.	The seat belt warning no longer works.
9.	Cruise works fine but only the brake pedal cancels it. I tried a couple of workaround’s for the clutch but they did not work.
10.	I did not have to do any wiring on the instrument cluster to get VSS to work. I just plugged it in to the old wiring harness. Actually I put the automatic sensor on the top of the manual gear adapter in the diff housing.
11.	Axles from the VR6 will fit the 5 speed manual trans.
12.	Backup light wiring and clutch starter interlock is like in the other threads. 

*Brake Pedal*: I had read somewhere that it was possible to only trade the pedal in the assembly and not the whole bracket to save some time and effort. This should work if your assemblies are compatible with each other. I spent an entire evening working on this with no success before I found the problem. It was totally my fault, and after I found it, it was embarrassing, but I wanted to help clarify things just the same. 

The photo below makes it painfully obvious why it won’t work in all cases, but I didn’t happen to look at the two from the side until hours later under the dash wondering what was wrong. The top lever is from my 2001 GLS, the bottom one supposedly is from a 2001 GTI. I really don’t think so, but not sure. The problem is the location of the pivot bolt on the left.










Since the same steps are required to change either the pedal only or the entire frame assembly, I would take out the pedal first and check to see if it is possible to just swap it out before I removed the frame. It may be possible to save quite a bit of work. Even less work on the Mk IV is to just leave the Automatic brake pedal and use it like many have done (myself included at this point).

*Removing/releasing the brake pedal*: The push rod that goes from pedal from the master cylinder is retained to the pedal assembly by a spherical end that is snapped into a plastic clip shown below. Whether you are going to change just the pedal or the whole assembly the clip will need to be released. Before you start it is advisable to hold the push rod into the master cylinder before you start. This is really easy to do if you look at the brake pedal frame assembly and the pushrod next the firewall. I pushed down the brake pedal with vacuum still available so that it would collapse more and put a screwdriver handle into a hole in the side of the frame to hold a large white piece depressed. It is not so apparent why to do this until you try it without. I didn’t get a photo of this but it should be obvious if you just take a look when doing the process.

The photo below shows the broken clip in the pedal assembly I received, but it illustrates the clip that needs to be depressed on the bottom right (red circle) to disassemble the parts. On a good part there is a finger on each side. I made a tool like what is shown in the Bentley, but a moderately large flat screwdriver (3/8 wide blade?) worked equally well, maybe even better. What I did was to locate the tip of the screwdriver at the clip, pulled on the brake pedal while prying the clip fingers back by twisting/prying each side alternatively until the pedal pops free. Then pull it down and out. 










*Clutch line clips*: I struggled with inserting the retaining clip on the master cylinder end for quite a while until I noticed that the clip inserts from the fender side and not from the front. If I had looked closer before I installed the master cylinder I am sure I would have picked up on it right away, but I did not see any mention of it in any of the write-ups and after it is mounted to the firewall it is not easy to see. Even thought I don’t have a picture, I thought I would make a note of it to help others. Look at the master cylinder before installing it and you should be fine. 
By the way, the dealer only shows one clip for the assembly in their break down but there are three total used; one at each end of the line and one on the bleeder screw. They also call it something else but I seem to have lost the bag. The o-rings are called a “Washer”(p/n 02F-141-143-A).

*Clutch Bleeder Screw*: My bleeder screw was fairly rusty. I should have done a better job of inspecting/prepping this part before installing everything, but didn’t. I was concerned that if I just tried to loosen it in place I would crack the plastic slave cylinder. The way the slave is made it is not intended for the clip to be easily removed with the slave the installed on the transmission. It might be possible to push out the clip from the bottom but I could not reach that very easily at this point. But, a little careful work with an 1/8 inch drill bit can make a recess that you can work the clip out from the top with a small pick or screw driver. It is not real easy to see in the photos below (sorry, but I was not able to get a good picture but you can get the idea), but the drilled area is just to the right of the clip and is only about .060 deep, which is just enough to let you get something under the clip and pry it out. Now you can pull it out to the workbench and clamp it to get the screw loosened. The picture also shows the power steering line routing I used. A little bending made it fit fine.










*Engine support*: OK, not that original since I got the idea from another post somewhere, but improved on it a bit. Since I had the VR6 project, and some work on a 1.8T coming up I went a little further, but it turned out to be really simple. Some scrap 2x4s and a piece of threaded rod, nuts, washers, and some hooks welded onto the end and then, there it is. I put two boards flat to support he load and provide a wider surface for the threaded rod to go through. You may want to use a different configuration or use a heavier cross piece to support the threaded rod, but I found this configuration to work well for me. To fit different engines just re-position the top boards and screw them to the crosspiece so that they wont move around. Drill holes as required for the threaded rod above the engine hoist loops for your engine. 










I did put a shim (Blue Circle) under the front ends of the sidepieces and drilled short recesses (Red circle) for the bolt heads on the fenders to help hold it into position and cut notches out for the rubber bumpers that the hood rests on when closed. 



















The location to drill can easily be found but fitting the boards and pressing down on them. You can then see where the bolts touch. I also sculpted out a little on the bottom edge away from the headlights to better fit the curve of the fender

One note for use, the boards do flex under load and that lowers the engine about the correct amount to remove the transmission. I put a floor jack under my engine and lowered the engine to gradually put tension on the support. I did most of the work with the jack removed for more room. When going back together I just jacked the engine back up into position. It is important to choose boards that have minimal knots to make sure that they do not break. I had no problem with standard pine but if you wanted to spend more for either “clear” lumber or even oak, that would be stronger. I used some scraps I had around. To raise and lower the new transmission I used a ratchet strap over the main cross piece and did the change entirely by myself with little problems. 

*Reverse lights*: As has been posted by others, the pin positions are more important than the wire colors, although the colors are mostly consistent, especially for the gasoline engines. I may have missed something where the terminals were called out for the backup lights, but thought that this photo may be beneficial showing where the Black/Green and Yellow/Blue wires were located in the connector. Just connect them to the backup light switch (after doing the other wiring under the dash) and there you are. 










I also cut the Yellow/Blue wire going to the ECU to avoid problems since this circuit was being used for something else now. Another hint I read somewhere; the backup light switch has the same connector as the brake pad wear sensors. You can cut one off of an old brake pad like I did. Works great.

*Shift Boot*: The one supplied with my kit was in pretty bad shape like some of the other photo’s I have seen on other conversions. I am not sure how long my solution will work out but seems to be fine for now. I cleaned the boot with isopropyl alcohol and then sprayed it with 2 coats of FlexSeal. Not like new, but much better than it was.

I hope these comments useful to others. There are many fine threads out there but seem to miss a few options that can be taken if you are not changing the ECU. Some of the points I made were addressing things that took me a little while to figure out that were not detailed in the threads I read and I wanted to give back a bit.


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## GreenVRMonster (Jun 28, 2012)

Hey I'm new to the community here, but I've been on the site many times and its helped me out. I'm having trouble finding information on this tranny swap, because i have a mkIV vr thats an auto, i have the whole car for a swap but the recipient car is a manual 2.0l, i know i would need to swap the cluster and ecu, or find a manual ecu. aswell as clutch master cylinder, but would the shift cables be the same? and if its already got the relay for the reverse light and cruise do i need to splice a wire from the ecu into one of those wires? any help would be appreciated, thanks


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## CoolAirVw (Mar 8, 2007)

So you reused your ECM with no changes? I assume your left with lots of codes?


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## CoolAirVw (Mar 8, 2007)

So you reused your ECM with no changes? I assume your left with codes? More than likely if you were to get a manual ecm your "flare" might go away. 

My tuner said he might be able to reflash a auto ECM with manual software, but it would be experimental.


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## SRB94 (Mar 10, 2009)

*Manual ECU time*

OK, so after making sure that everything was working correctly i decided to go ahead and swap the ECU in an attempt to get the flair to go away on shifts. Success!!!. Other than the re-coding of the immobilizer, etc., as described elsewhere and adding the connection between the clutch switch and the ECU everything was set to go from the other posts. The Auto ECU does set errors due to there being none of the sensors or controls that it is looking for. That kept the CEL on, but everything worked fine otherwise.
In addition to the flair being gone it is also easier to drive away from a stop. There seems to be some "lost motion" in the throttle linkage implementation for the automatic calibration that is not there on the manual ECU, coupled with a slightly different response curve that makes things work out much better. Only having it installed for a week it is hard to say but the fuel economy seems to have suffered slightly, but that could be me playing with it more. Bottom line is that i recommend it.

*Basic Steps as follows:*
1. Remove Auto ECU
2. Install Manual ECU
3. Connect One side of the clutch switch to the same common as the brake switch pin 2 (blu/blk).
4. Connect the other side of the clutch switch (CVVV) to pin 39 (red/white wire) of the ECU. I used a now unused red grey wire that used to go to pin 11 on the TCU, but you also can use the connector right above the relay panel as described in nosborn94's writeup (link to p. 4 below) in a comment from sp1249 on page 5
5. Update the immobilizer (you will need the VCDS software or a friend at the dealer for 5-8).
6. Adapt the Throttle body
7. Set up cruise control.
8. you can try to configure an Auto ECU to Manual but I gather that this will only work for the Diesel controllers.
Your done. Took me a couple of hours to finish up.

Please take the time to check your individual wiring against the Bentley before you start. I found most of the wire colors to be correct in other posts of similar (gasoline) cars for the most part, and the pin numbers were correct, but it would be nice to not have any surprises with the smoke leaking out so check first. A good review also helps you to understand what you are doing, at least it did for me.

I did make an error on the fluid I used. Just changed it yesterday to the Penzoil Syncromesh ($7.99 / qt qt Advanced) and seems to work well but still have a little crunch in second from time to time if I am a little late on the clutch especially at high RPM. Maybe it needs some time to work into the syncro's. Time will tell.

For a great discussion with lots of details and pics see http://forums.vwvortex.com/showthre...-swap-on-my-2001-Jetta-2.0-(AZG)-silver/page4. He has done a great job of documenting his entire process for a 2.0, but most of it applies directly to the VR6. The purpose of my post is to break it down to a more simple summary in case you are overwhelmed by all the detail on most of the posts. It really is not that difficult, but as coolairVW said in one post, the brain work is one of the hard parts. But realistically, I don't know how you would put together a decent set of instructions without all the detail. Read up before starting, and many, many thanks to those before me.


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## vdubbfourlife (Jan 5, 2007)

*Please help! *

Hello, I am hoping you're willing to give me some more details in regards to switching ECU's from the auto to manual on my 01 MK4 Jetta VR6. My good friend and I have come a long way with this project and do not want it to go to waste. I want to finish the tranny swap the right way by switching the ECU's over to prevent the idle flair when shifting, and the small lag when taking off from a stop. (I've read about them) 
I have confusion on how to connect the clutch switch to the brake switch, and how to update the immobilizer. Also don't know what you're referring to when you say "adapt the throttle body". 
I would greatly appreciate your help bro  It would mean the world to me if I get this thing finished after all of the work we've done. 

PS: Are you willing to talk to me about this over the phone? It is my birthday tomorrow (the 21st) and we are trying to finish this project before the day is over. (Getting the car ready for a VW car show on Sunday) 

Thanks for any help, 
Curtis


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## Serpent7 (Dec 24, 2003)

I have a 2001 Jetta vr6 auto that has intermittent transmission shifts. I am considering swapping to a 5 speed. Reading this post has inspired me! Before I start I was thinking about putting a parts list together and sourcing them before I get started. Can anyone help with that here? At least a list of parts to get the 5 speed mobile. Thanks


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## CoolAirVw (Mar 8, 2007)

Seems like you could get the answer to this simply by reading this thread, but here's a short list..

trans and everything bolted to it including shifter parts and mount bracket, reverse light switch and reverse light switch pigtail harness.

axles and axle bolts. 

clutch pedal assembly, clutch pedal switches and related Pigtail harness's.

Brake pedal (don't have to change this, but it makes the conversion nicer)

Engine "tin" that separates engine from trans

Clutch. 

I have never converted a VR6 but you'll probably need a computer to make it right. Changing computer require some "stuff" to accommodate the immobilizer.


Also read this monster thread.. 

http://forums.tdiclub.com/showthread.php?t=151516

The info in this thread is specific to a tdi engine and although most of it will be "dead on", some of it wont apply.


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## SRB94 (Mar 10, 2009)

*Axles not required for V6 swap*

Just getting back to the forum after a long absence and noticed this question. In my case I found that the axles were the same between the VR6 auto and manual trans.


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## Pitchblack151 (Aug 28, 2014)

*Mk4 jetta triptonic swap to 01 wolfsburg 5 speed*

New to this thread but I have a 04 jetta 1.8t and it has about 129k and starting to notice my trans is going
Out and I bought a 01 wolfsburg 5 speed trans with this trans work and will I need a new crank??


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## mujjuman (Jul 29, 2004)

Hey man thanks for all the great information in this thread. I have the same car as the OP (2001 Jetta VR6 12v with the O1M auto trans) and my auto trans took a bad hit. 

I'm thinking of swapping in a 5MT or 6MT. I'm guessing the O2J 5MT will fit, based off the results in this thread. That's the MT from the 1.8T right? Just want to make sure. I'm not planning on going FI or building my VR but I'm planning on keeping it for another 5+ years. What 6MT can be bolted on here? I remember seeing a 5MT to 6MT swap here years ago. 

So my state requires the CEL to be off for the state inspection to pass (New York). I wanted to know how easy/hard it is to flash the automatic ECU? Is it too complicated to get it to work like stock? 
Otherwise, how would someone swap in a manual ECU and code it to work with the car? 

Please help. Thanks 

mujjuman

[EDIT]

nvm, going with the 5spd swap instead. i learned that the 4cyl transmissions do not bolt onto the VR6. you will need a transmission designed for the VR6 (for the record and anyone reading this in the future)

i have heard conflicting stories about whether the VR6 axles from the auto will fit with the manual trans... i am holding off on ordering new axles for now and i will report my results. 

not sure where i can find the 'pigtails' that go on the switches on the transmission and the clutch.. if someone knows part numbers and where i can order, please let me know asap!

[EDIT x2]

Ok so the swap was done on my car. I ended up buying aftermarket axles (hope they last) but saved the original OEM auto VR axles just in case. 

The clutch switch is not wired. Only the reverse lights are wired. As a result, the cruise doesn't work, and I can start the car without depressing the clutch. There is also a rev flair in between shifts. 

My auto ECU was flashed with manual programming, and I have no CEL, and no other error lights on my car. ASR works fine, as tested when it was raining (lol). There is also no lag from starting in 1st. The only problems are the rev flair or rev hang while shifting gears and cruise control not working. The rev flair is a bit annoying because it makes my 3rd gear grind, and I'm afraid of ruining my clutch prematurely. 

I'm wondering if the OP had his clutch switch and cruise control wired prior to swapping out his ECU for a manual version. Honestly the wiring looks too scary for me to tackle right now and is confusing me. How do I even connect the wires to the back of the clutch switch?


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## FREDDO (Sep 25, 2015)

*Help!!!*

Hi there, 

Does the ECU have something to do with a power windows????

help me thanks


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## LouieVDub916 (Mar 29, 2016)

mujjuman said:


> Hey man thanks for all the great information in this thread. I have the same car as the OP (2001 Jetta VR6 12v with the O1M auto trans) and my auto trans took a bad hit.
> 
> I'm thinking of swapping in a 5MT or 6MT. I'm guessing the O2J 5MT will fit, based off the results in this thread. That's the MT from the 1.8T right? Just want to make sure. I'm not planning on going FI or building my VR but I'm planning on keeping it for another 5+ years. What 6MT can be bolted on here? I remember seeing a 5MT to 6MT swap here years ago.
> 
> ...


Did you ever figure out that clutch switch wiring?

Sent from my C6725 using Tapatalk


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## ConvergenceFreak (Jul 23, 2015)

LouieVDub916 said:


> Did you ever figure out that clutch switch wiring?
> 
> Sent from my C6725 using Tapatalk


In the massive thread CoolAir linked to on TDI club, there is a bit about how the brake and clutch switches are adjustable, On my 5 speed swap the clutch pedal switch was totally out of adjustment and the Cruise didn't work at all. I figured it out thank to that thread and adjusted it. I suspect, if all the wiring here was done correctly, that the clutch pedal switch is simply out of adjustment. it will simply need to be take out of it's holder, pulled on, or pushed in, I think the action is reversed up where it lives. You will hear a lot of small plastic teeth, clicking and you pull it out. Pull it (or push it in) out a little, insert and try again, until it's engaging/disengaging with the the pedal action. Best of luck.


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## reiecco (Jun 15, 2017)

I have this exact same car that I just put the five speed into everything works but I have CEL/ASR lights on? Can?t smog in California with that going on. I have the manual ECU in as well, but when it comes to the wiring that is stated here I?m not exactly sure where everything is. Also, I have the steering wheel that controls The radio volume and changing of CDs and stations, as well as to cruise control buttons. I?m wondering if the gentleman here has that steering wheel too...I tried to PM him but this thread is pretty old so if anybody could help me I would greatly appreciate it. I just need more detail on the ECU wiring. I'm electrical challenged


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## mujjuman (Jul 29, 2004)

LouieVDub916 said:


> Did you ever figure out that clutch switch wiring?
> 
> Sent from my C6725 using Tapatalk


Massive bump. 

Yes I did!! I bought one of those blue clutch switches and installed it behind the clutch pedal. The wiring itself was not bad at all. I dont remember exactly what I did but the wiring was pretty easy. I used lots of diagrams found by searching the forums and random sites online. I wish I saved all of this info to share. 

But once the switch was correctly installed, the rev flair instantly went away and my cruise control was working again. 

Some advice regarding the blue switch... it is very flimsy and the internal mechanism can break very easily through "normal handling". You wont even realize it. Be very careful when adjusting the black stalk that sticks out of the switch.

[edit]

check out this post:
https://forums.vwvortex.com/showthr...ZG)-silver&p=72748796&viewfull=1#post72748796

I used this to help me wire my reverse lights and my clutch switch (blue switch)


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