Originally Posted by swissfrank

1) yes it is possible. A e39 540i 6 speed manual transmission would bolt on to your engine, you just have to change the rear output shaft to have it mate properly to the transfer case, new flywheel and possibly the bell housing.

2) your current bmw computer that controls everything is useless, wiring harness useless, any misc control units, useless. New wiring harness = very expensive, dsc, tracation programs, etc etc etc would all not function correctly, there are aftermarket alternatives that will bypass these obstacles but very costly. If this were an off-road vehicle only, go for it.

As far as cost, it would be far cheaper to grab a reman auto transmission as even though it is physically possible to change out the auto box for a manual, it will be far more costly than servicing you now retired autobox, not to mention doing a swap will be far more time consuming.

Say a pressure plate and clutch disc alone is roughly $1000, this doesn't include clutch pedals, or anything else, these parts will add up quite quickly.