I have a 3 speed automatic in my cavy 3.1 I know they also make a 4 speed. Has anybody ever made the swap from the 3 to the 4 speed? If so does anything else have to be swapped out such as the computer?

the only thing the computer controls on the tranny is the TCC solenoid.

You can swap to the 440T-4 or the newer 4T60/65E tranny but it requires some modifying/fabricating of the tranny mount, also custom axles. the newer electronic trannies need a controller, you can get that for about $900 at www.wot-tech.com. The 440T4 weighs like 200 lbs and is found in older Luminas, Park Ave's and other random cars.

Your best bet is to swap to a 5 speed manual, much easier, lighter, stronger and better fuel economy.