What do you mean 'swap everything'? Are you planning to swap the whole engine in, or are you looking to just swap the turbo, manifolds and the like? Either way you're going to run into some snags. Since you listed the transmissions as well, I'm assuming you're planning to swap everything.
First off, You've got a 89 car, and a pre-87 GTE. This is going to cause issues in several issues. Some of the sensors won't work (injectors for example), unless you bought the ECU and full wiring harness. If you have the wiring harness, all sensors, and (maybe? I don't recall if it's needed) the dash harness too it should be cake.
If you do some searching, I've posted a lot of cross-forum links and quotes and info about NA->T swaps.