2000 BMW 540i Touring 6 Speed

After less than 2 years of owning my E39 Wagon, it has just about spent as much time up on jack stands as it has on the road.  However, now that it is “complete”, it is one heck of a ride.


Last winter I set out to get the suspension all squared away.  I had bought the car fairly cheap, but it gave me hell from the beginning.  One of the rear suspension bushings had worn out causing a terrible vibration upon braking and between speeds of 55-65MPH.  A week after I bought it the water pump had a catastrophic failure the day we were supposed to go out of town, forcing me to take it to the dealer to let them replace it.  Over last winter (2015-2016) I put it up on jack stands and replaced every suspension component I could: powerflex bushings everywhere, beefier swingarm, subframe bushings, KW coilovers…..the whole lot.  It really tightened up the ride.


Towards the end of the summer, the radiator started leaking and the automatic transmission was acting strange, making it a bit of a pain in the ass to drive.  Things sort of lined themselves up when a wrecked 2000 BMW 540i 6 speed sedan popped up on the forums and I snagged it for a pretty good deal.  It would have everything I need for a 6 speed swap in the wagon and I could swap the good radiator for my bad radiator. I am now parting out the rest of the wrecked car, in hopes of at least breaking even on my investment.

In case you were wondering why I would do such a heavy swap.  I have always been a fan of manual transmission cars.  It is a much more engaging experience and the whole V8/manual transmission has that good ol’ muscle car vibe even if it is a station wagon.  It also helps that they never made a 540i wagon with the Getrag 6 speed.

This swap wasn’t the easiest and in hindsight I should have bought an automotive lift for the shop first.  If anyone stumbles across here looking for advice and guidance on how to do this swap in the future.  That is my first bit of advice and I am shouting it at you.  It is awfully tight and you have to get quite creative to actually pull the transmission out from underneath the car.


I will briefly run through how I did this swap and comment on the parts I had trouble with. There is an excellent write up on bimmmerforums by geargrinder.  His help was invaluable throughout this swap.

Pulling the physical bits from the donor car was fairly straight forward and did no cause too much trouble.  The only time things got interesting was when I was trying to get the transmissions out.  A few bolts on each transmission managed to seize themselves into the engine and the heads stripped out.  Naturally, it was always the bolts that were hardest to get to: the very top bolt or one other that was hidden by something else.  Another issue I ran into, that is amusing now, was getting the transmission stuck underneath the car because it was jacked up high enough……back to the advice of “GET A LIFT FIRST!”

I was hoping to be able to use the flywheel, clutch and pressure plate out of the donor car as I was told they only had 10k miles on them.  Upon inspection they looked beat to hell.  I went with a JB Racing lightweight flywheel.  The nice part about it is the wear surface on it is replaceable, unlike the stock BMW flywheel.  While the transmission was out, new seals and fluid were put in it, new rear main seal installed.  Once all that was squared away, it was onto the wiring.


This is where geargrinder’s “6 Speed Swap” instructions were invaluable.  The other part that made this less of a hassle was having a donor car to actually see where the wiring and pins were coming from and where they were going to.  In fact what I did for my wiring was snip the wires from the donor car and pull the pin from the connector and use it as a pig-tail  to wire into my car.  The best part of this, is when I reference wiring diagrams, all the wires are the right colors.  Now not all of the wiring can be done exactly as to factory, well not easily or even with a moderate amount of effort.  I got a little creative and found wires and connectors from the wires left in the gear shift console.


It all looks like voodoo when its on the sheet, but fairly simple when you can physically look at it and compare to the diagrams.  There are notes there where I have made changes in my system.

While the wiring is good enough at the moment, I have found 2 things that need to be addressed.  My cruise control is intermittent and not repeatable  regularly.  In fact it does not work more than it works, I have yet to get it to go in 6th gear.  More testing is needed.  I also just found out that the reverse lights do not work.  While not a major issue, it does make it quite difficult to see at night in reverse.  I will grab my multimeter here in a few days and source the fault.


Now the physical bits went in the wagon.  The transmission had to go in twice.  Because I was using a motorcycle jack and a good bit of Kings Point engineering, the first time did not go too smoothly.  In fact after I got the transmission in place, I went to test out the clutch to make sure it was operable before installing the rest of the drive train.  Pressed the clutch, and with a solid pop lost all pressure in the pedal.  I look underneath the car to just see oil pouring out of the bottom of the bell housing.  Turns out the pin that holds the clutch pivot arm had popped out during the installation and the clutch slave cylinder blew.  That ended up being 3/4 of a day wasted, with another whole day of pulling the transmission and reinstalling.  Again, with a lift this never would have happened.

Doing the coding on the car was a thing of “Past Andrew” really screwing “Future Andrew”.  I figured it would not be that difficult to find someone to do the coding on the computer.  Turns out that there were no enthusiasts I could find locally to help me out.  However, as it happens, I was driving down the Boulevard and stopped into the local BMW shop just to ask to see if they could do it.  Thank god they could, because I had run out of options at that point.  The owner, Brad, of BMUU in Colonial Heights, VA really saved my bacon on this build.

There were several little things that Brad taught me during this whole coding process.  For example: When he came over to do the coding and we started the car for the first time, the brake lights were constantly on.  I had no idea that the brake light switch on the pedal has to be adjusted when you swap over new pedals.  That seems like one of those small things I never would have figured out on my own.  The other one that would have been amusing without Brad’s help was trying to get the key out of the ignition.  Since the auto trans gearshift interlocks with the key in the ignition lock, you have to get creative with zip ties on the cable to simulate that the gear shift is in park.  Again something else I would have struggled with.

We had a few nights of struggling to get the computer to talk to my car’s computer to do the coding.  Since the car was “driveable”, just no car aids (traction control, abs and the like).  I dropped it off at his shop for him to sort out.  After he sorted out the chassis modules, I mailed out the computer to Kassel Performance for a tune and to get rid of my check engine light.  This also sorted my strange starting issue of having to turn the key to the on position and leave it there for a few seconds before starting the car.


After that was all done, I had tried to adjust my rear suspension to lower it, to help square up the stance.  It seemed to be alright but when I took the car for an alignment it appears that the car adjusted itself back to stock height.  Again, Brad at BMUU hooked me up, and we coded the car so that the SLS airbags lowered themselves to the proper height.  Another clutch bleed while, we had the car on the lift at BMUU and the car is squared away and looking damn good.


This was one of the coolest projects I have done in my garage.  The car is a blast to drive, and so much better with the manual transmission.   I am sure I will constantly be wrenching on the wagon, but what else do you do with a hot rod.  If you need service and you are in the Central Virginia Area, I would definitely look up BMUU in Colonial Heights.  If you need parts off of an E39 sedan, hit me up, I have a whole car to get rid of.




3 thoughts on “2000 BMW 540i Touring 6 Speed

  1. Victoria Saxon says:

    You have beautifully written your experience and issue you have faced with your used car. However before purchasing any car whether it is old or new, it is better to inspect it. Otherwise in future, you might have face lots of problems which is the main reason for spending lots of money on your car for repair it. Well suspension issue is very common in cars. This component get always abused due to potholes rain winter summer etc. Hence maintenance is definitely unavoidable. Only a good mechanic can solve your issue. For more information you can visit https://dellsservicecenter.com/reasons-for-bmw-suspension-issues/ .


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