A bit of an update... Found a 6MT '09 335i down in Austin, Texas and picked it up for a good price. The car was delivered to my house last Tuesday, it runs and drives. I started pulling apart the front of the wagon, and the n52 is pretty much ready to be taken out. Just have to pull off all of the wiring, disconnect the driveline, exhaust, and pull the motor. I have to rearrange my backyard a bit to put both cars in a good spot to swap everything from one to the other, but as soon as that's done the swap will be continuing.
For now, I've been messing around with NCSExpert and reading a bunch of modules, getting to know the program a little better. I think I found the section that's going to be the key to getting the wagon to recognize the n54 and the 6mt swap, but I'll be doing a little more digging as the week goes on. Will upload a few pictures of both the wagon and the 335i soon!!
Also, I'll be parting out all of the suspension and drivetrain from the 328i so if anyone is interested PM me.