What he wants to do is use a manual donor car to convert an automatic M3 to manual, while wanting to have a complete other car to be able to sell as a whole (or maybe for his wife to drive for all I know). Since there are lots of Auto -> Manual swap threads and guides, he's not interested in another. Instead he wants information about how to reassemble his donor car into something road worthy. ( Also posted at bimmerforums. )
I have done this the other way around on different cars several times. The automatic to manual would possibly be more difficult and probably is. I know that trans fluid needs to go to radiator. So a new radiator would be a neccesity. Also the linkage to the throttle setup. You are gonna need a throttle setup from a manual to install. So that your transmission and gas pedal can communicate. Also the input shaft will be different. The input shaft from the trans sits inside a bearing in the crankshaft. You will need a different driveshaft, crossmemeber, and thats without even tearing into it. Thus, you will need much more. I would only do this if somebody bet me $2000.00 that I couldn't, seriously. When I did this for the first time, I had one of each car side by side. Same model car and everything except one man. and one auto. So I took out the dash of the manual and extracted the pedals and linkage. This made things so much easier. I had all of it there. If I were you I would buy a scrap car with the essential parts to alter the other with. Leave the automatic the way it is. You will spend as much money chasing parts as you would if you just bought a donor car and left the one car alone. Because if you do both you will be searching for parts for both. GUARANTEED!
yes i know, it seems common so far to to being shunned for this, i know that the manual trans is the preferred choice an would be mine but due to a "Cerebral Palsy" that effected my right leg a manual might not be best thing for me in a daily driver... i'm not sure how else to put it
Sounds like a fun project. Go ahead and take it on. I am sure you'll find some hurdles along the way that you'll end up overcoming. Take a lot of pictures and you will have yourself the first ever online DIY writeup for a manual-to-auto swap in an E36.
P.S. It will be a lot of money, time, and work. There is a risk you'll end up hating yourself for trying.
it's really not worth the effort
the wiring, the torque converter and other things can really be a bitch
you also need the different water radiator with the oil cooler
the pilot bearing needs to be removed from the cam shaft
you need a shorter drive shaft and an automatic differential case and you need the ecu
oh and the gear lever