You can bolt on any D-series Tranny aside from the D17/Bastard-D Trannies on your engine. It all depends on your gearing preference which would depend on when you do with the car. You can even tear the Tranny apart and slip in different gears off different D Trannies to get the gearing you want. But there is no use in messing with it if you don't know exactly what gears you want.
Also, for the mods you have, a new ECU is not needed. However, resetting your ECU by disconnecting the battery for a couple minutes is recommended seeing as your ECU will need to learn the new sensor readings and learn to compensate.