Thank you for joining me again on this second part of the 6-speed gearbox swap on my BMW e39 Touring. If you haven’t read the first part and the introduction of the vehicle, I invite you to read it here and here.

gearbox detail shot
Replaced shifter seal on GS6-37BZ

I haven’t spoken too much about it in the first part but maybe the most important reason why I decided to complicate things by switching to a 6-speed gearbox (over repairing the original 5-speed), is to have better fuel mileage. Even though driving pleasure and shift feel is important to me, the time spent driving for fun on track or small country lanes amounts to a very small portion of the total kilometres driven with the 5 Series. I’d say 85 to 90% of my driving is done on motorways, another 8-9% is done on smaller roads (dual carriageway), and maybe only 1% can be considered as drives for fun. 

motorway driving
e39 Touring in its natural habitat

With fuel prices being what they are in Europe, it’s easy to understand how even small savings in fuel consumption can have a big impact on the running costs of the vehicle and why it is so important to me. Better shift feel is just an added bonus for those last 10% not spent at cruise on the motorway. 

e39 gauge cluster
German autobahns are ideal to test the long distance abilities of the e39.

Furthermore, with global warming being everyone’s responsibility, I feel that as a professional in the automotive aftermarket/repair business, I have a duty to show what can be done with older vehicles to make them more economical and longer lasting. I don’t believe buying a new Euro6+ compliant vehicle now, and replacing it in two years time by a plug-in hybrid, to replace it again two years later by a full electric is the solution to a green future. Those vehicles might have better tail-pipe emission figures but the grey energy needed to build those cars and the maybe not green electricity used to power them far outweighs the emissions of older vehicles or old cars with reengineered powertrains.

Car in garden. Rear view of car with trunk open. Dog lying in trunk.
e39 daily driver duties

That being said, let’s jump into the swap. 

Before bringing the car in the workshop, I started fabrication on the gearbox’s crossmember. The BMW e85 Z4’s crossmember doesn’t fit the e39 chassis, and an e39 5-speed’s crossmember doesn’t fit the GS6-37BZ gearbox. There may be an OE-part number to solve this problem, but for me it was quicker and more cost effective to fabricate my own crossmember. For materials, I used 8mm thick steel tow hitch reinforcement plates I had lying around. Those plates had useful obround holes in them so I cut and welded where needed to re-use those holes on the mating surfaces. That way I was making sure to have the adjustability with the gearbox rubber bushes and with the e39 chassis. 

mig weld on steel
Crossmember weld

Fast forward into the garage. With the car still on the ground I removed the wooden shift knob, the leather shifter boot, and the insulation foam around the shifter, revealing the hole in the transmission tunnel. I then put the car on the hoist and removed the exhaust from under the car, leaving just the exhaust manifold on the engine. I took off the various headshields to give me access to the propshaft and gearbox. The next task was to remove the propshaft (unbolting rear CV joint, center bearing, front flange at rubber flex disc), which is all easy to do on a BMW e39. 

shifter linkage hanging under vehicule
shifter linkage hanging under vehicule

Having now complete access to the gearbox, I removed the different connectors on the gearbox (reverse switch), and freed the cables attached to the gearbox housing, to finally start unbolting the gearbox bellhousing from the engine (various sizes External Torx bolts), using different lengths of 1/2in and 3/8in extensions. The starter motor was also unbolted as well as the clutch slave cylinder. They can both stay in the car and the cables/hydraulic lines don’t need to be loosened (The original clutch slave cylinder fits the GS6 gearbox without modification. 

bolts on the ground
The bolts of the gearbox’s bellhousing in order

Placing a transmission jack under the S5D gearbox, I unbolted the last two bolts, pulled the gearbox gently backwards and it came off the engine/flywheel without resistance.  

gearbox under vehicle
S5D-250G removed

With the 5-speed gearbox out of the car, I could place it next to the 6-speed, and compare total lengths with their respective propshafts bolted onto them. Lengths seemed identical which is what one wants.

two gearboxes next to each other, blue welding machine above.
S5D-250G next to GS6-37BZ

I went back under the car to remove the clutch and flywheel. They came off easily and I took the opportunity to inspect them. The flywheel was worn but still usable. The clutch friction plate was definitely on its last legs though, and I’m surprised I’d never had clutch slip before. On a side note, I think the clutch was the original clutch of the car. I’m impressed it lasted until 315.000km without slipping. I guess it could be expected from a large car doing mostly motorway miles and otherwise being downshifted with heel-and-toeing. But still. Always learning I guess. 

clutch friction plate and flywheel
Worn clutch and flywheel

I now had a direct view of the back of the M52TU engine with its eight bolts crankshaft’s flange. Even though it was still dry, I replaced the rear main seal preventively. To remove the old input shaft bearing in the crankshaft -because I didn’t have the proper extractor- I used the method consisting of stuffing soft material through the middle hole of the bearing which pushes the bearing out of the crankshaft when the space behind it fills up. I used a combination of folded duct tape and grease. Took 20 minutes for the bearing to come out, but it worked. 

rear view of M52TU engine
Rear main seal and pilot bearing replacement

It was now time to start bolting the new parts to the car : M54B30-e85 Z4-spec flywheel, new clutch kit, and the 6-speed gearbox without its shifter linkage. Using the transmission jack and wooden chocks, I made sure the engine and transmission were at the same angle relative to the body that they were before, before final welding of the gearbox’s crossmember. This is important to ensure proper propshaft’s CV joint angles which if not respected can create vibrations. My crossmember might not be as lightweight and pretty as the original aluminium crossmember but it does the job of holding the gearbox where it needs to be. I came this far in one day. Time for a beer, a walk in the forest with my dog Kairo, a good night’s rest.

6-speed gearbox bolted to the chassis
6-speed gearbox bolted to the chassis

Day two of the swap started with work on the shifter linkage. The shifter linkages and aluminium support arms from the two gearboxes are different enough that the e39’s linkage and support arm wouldn’t bolt up on a GS6 gearbox, but the e85 Z4’s aluminium support arm would fit the e39 chassis if shortened 67mm, as they both are held by a similar cylindrical rubber bushing. I therefore used my AC/DC tig welding machine to shorten the Z4’s aluminium support arm and shifter linkage. That way, I retained the original mounting points on the gearbox, and gained the extra short shifter throw of the Z4 (compared to the e39’s notoriously long shifter throw). When the welding was done I bolted the shifter, linkage and support arm in the car. I now had a working 6-speed gearbox in the car. The only thing left to do was to link the gearbox to the differential with the propshaft. 

Shifter support arm in vice, welding machines on the ground
Shortened Z4 shifter support arm about to be TIG welded

Trying to keep the car’s down time to a minimum (daily driver remember?), I’d previously purchased an e60 530i manual’s propshaft, as well as an e39 520i Touring’s propshaft in Dutch junkyards, and I’d already mated the front half of the e60’s shaft to the rear half of the e39 520i’s shaft. But, when I came to bolt the hybrid propshaft in the car, I realised the CV joint’s flange of the 520i’s propshaft had a smaller BCD (smaller diameter bolt pattern) than my 523i’s differential flange. Thinking I’d revert to using the rear half of my 523i’s propshaft, I dismantled the propshaft again, only to be stuck again when I tried to assemble the e60’s front half to the 523i’s back half. The splines between the two halfs didn’t match. Back to square one, propshaft in two, I tried to use the CV joint of my 523i on the rear half of the 520i’s propshaft. Deception again, splines didn’t match here as well. Common, did BMW engineers really have that much time on their hands at the time to design so many different propshafts for their cars?

two propshaft splines
e39 520i splines vs e39 523i splines

An obvious solution here would have been to bring the e60’s propshaft and the 523i’s rear half to propshaft specialists and have them weld the 523i’s rear flange onto the e60’s, or source a 520i’s differential and bolt it up in the car. But that would cost more money and would immobilize the car for a few days. Less than ideal for a swap meant to be done on a long weekend in-between a busy work schedule. I therefore went a bit ‘ghetto style’ and drilled out my differential flange. I went this route because I wanted the car to be back on the road as soon as possible. I also judged the power of my engine to be low enough and material left on the flange to be sufficient that it wouldn’t be a problem. I do not recommend doing this to your car, especially if you intend to abuse the drivetrain (drift or drag use). I also do not recommend this option if you don’t have the proper tools and skill to drill evenly. Anyway, with the differential flange’s bolt holes bored out, I was able to use the e60’s front half with the e39 520i’s rear half and bolt everything to the car. After that hurdle was overcome, it was only a question of mounting the heat shields, the exhaust system, and leather shifter boot and going for a test drive. 

First noticeable change, the Z4’s shifter is shorter (the original e39’s shifter is quite tall). The throw is much shorter (which is good), but the gears are easy enough to find that it doesn’t feel like a cheap aftermarket short-shifter (important detail). There’s nothing worse than an excessively short shifter throw that makes it hard to find gears. Driving the car around town, the e39 feels more alert and responsive thanks to those shorter gears (first to fourth). Just going through the gears, I can bring the car to the 50km/h speed limit quicker while using less rpm, which makes the car feel lighter, like there’s less weight to pull. This also means that using full throttle to accelerate on the motorway, the car feels noticeably quicker. Once at cruising speed, in sixth gear, the engine rpm is noticeably lower than before but the M52B25TU, with its recently serviced Vanos (BMW’s variable valve timing system) still has enough torque low down to pull the car. On the motorway, at 135km/h the engine is at ca. 3000rpm, which, to me, feels like a sweet spot for torque and economy. 

6-speed shifter in e39
Finishing touch

Driving the car on my usual itineraries, I witnessed an average saving of 1L/100km at motorway speeds, even more still with tail winds (somehow, with the 6-speed, the car can make better use of the reduced drag tail winds offer). On dual carriageways, the saving is even bigger with a record low of 7.3L/100km (with 245-40-18 Michelin Pilot Sport 4 tires), a number I could never have dreamed of with the old 5-speed. I’m also happy to report I haven’t encountered any fault codes, everything works just as before, cruise-control included. 

e39 gauge cluster
Lowered rpm means better mileage

To summarize, this 6-speed swap is probably the best modification I did on my car and I cannot recommend it enough to fellow e39 owners. Especially to those looking for more connection with the car, or those looking for better fuel mileage. It really makes the e39 chassis feel ten years younger than it really is. I know doing a swap like this requires certain skills and tools (welding) but, if you plan on keeping your e39 in the long run, I’d advise you to look into this swap. I also hope this kind of modification will help people driving different vehicles reflect on the way they see and use their vehicles; that it is possible to improve and upgrade older cars to make them relevant in today’s climatic and economic challenges.  

man in front of car with open hood
A happy e39 owner