This is a good writeup by Carl Nelson of La Jolla. We have a version of this in our tech section, but this is a bit more complete. It's not an overwhelming project, but everyone who has done it is glad they did. I'm looking forward to putting mine in.
http://bmw30cs.blogspot.com/p/5-speed-conversion.html
http://bmw30cs.blogspot.com/p/5-speed-conversion.html