m52 auto swap into a manual ti??

[KTEC]

I recently bought a 98 5speed ti with a bad engine. I found a 96 328 auto with a low mile swap. I want to keep the car 5 speed and wonder if I can use the engine and harness from the 328 to complete the install. I thought I read somewhere not to mix the 2 (auto harness in a manual car)but I want to find out for sure and if it is not a good idea why?

I am a master tech (not for BMW) so if it is a matter of removing the extra auto trans wires or something like that I can handle it. Any info wold be great.