Hmmm, well you need to check what parts differ. If the driveshaft is the same, you are in luck. Then you need to swap the box, including clutch. Swap the pedal box, add the hydraulics for the clutch and add 1000 small parts for the gear linkage. Once that is all done, you need to check the differences in wiring, and adapt that to be as close to the manual as possible, then get a vin from a manual and recode the entire car to manual spec...
Here is the most complete writeup on the net:
http://forum.e46fanatics.com/showthread.php?t=659314