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B10alia has the right idea, have the engine ready and set up with the proper components on hand and ready to go. There have been several guys/gals which have put a manual transmission in a vehicle that had the auto computer without any issues whatsoever so that is not the issue, it is making sure you have all the parts needed to put the whole thing together.B10alia has a very good starting list he needs and would recommend you follow (means of getting the components is up to you, a donor car is always a good thing, pull and swap everything at once is always a plus), but remember, you need the pedal assembly specific to your car, someone else knows the specifics of that, not sure which models will work or if she happens to be a year specific setup. Being a 1990, as a T1, your parts list could be smaller, turbo pistons, turbo rods (always be safe here), forged 2.5 crank if you can get one, and turbo head and camshaft, T1 computer you mentioned, wiring harness, manifolds, turbo, and a few other turbo items on the list.