A340 automatic in a manual MKIII body question

[Jay C]

I did a quick search and found some information but i still have a quick question. The car i purchased is being delivered in about a week. It was a project car for my father-in-law who was going to make it into a track car (but switched gears). It is a 89 manual MKIII body (shell) with a 89 engine and auto tranny (not installed). My question is what changes will i have to make to get it to work properly? I have the shifter, drive shaft from A/T to carrier bearing (as i hear they are different lenghts), and both an A/T and manual ECU. I am hoping not to have to cut the wire harness but need everything working correctly as i live in PA which has both safety and emission inspections. Furthermore, i do not want to do any modifications if at all possible that would make it harder to swap back in a manual transmission (as this is what i prefer to drive) once funds are available and i know the engine is running properly (as this is my first concern). Thanks in advance for any advice.