You will need a T4 in order to synch everything, it can be a can of worms if the new computer and the old one do not recognize each other. If you are just doing the engine/transmission/tcase then you should not have a new computer but can use the old ones. You will still need some time on the T4 to get it all straight. i would find an Indy shop that has time to fiddle with it or the stealership will gig you for some serious bucks. What was the quote for a new engine from the dealer $26K.
The computers will need to record the new serial numbers of the components that you are installing. This will require a T4 to reset everything and get it going. Easier than trying to get a new computer working with an old one but still may cause you some headaches.