I will need a different ECU even though its still a DII? ....
Yup. TC will find that the mounts dont line up with the frame because the tranny is 8mm or so longer.Pump length is different, brackets are different to accommodate the 1/2? longer pump . Axle housings are different to keep the pinion angles correct.
I agree about the rebuilt trans but I like the price of a junkyard one better.