Well here are some things I ran into (4th Gen specific):

- All you have to do is unplug the Auto-Tranny Computer, Engine ECU is fine
- Need to wire in the reverse lights (if you want them)
- You will have to figure out how to get the Cruise Control to work again... took me a while
- Find a way around the clutch pedal switches (for engine start and cruise)
That's all I can think of... not too much going on with the electronics on a tranny swap...