Got the engine done and dropped in.
The PCM is going where the coolant bottle is. I will have to get a smaller one and relocate it. It should fit nicely there.
This is what I'm using for my fuse block.
Trans and transfer case are in. Thanks to the engine mount adapters, everything lined back up in the original locations.
So far the only things that didn't bolt back up are the trans shifter linkage and the exhaust. The new trans has the module on the side so the bracket hits it. The exhaust should be an easy fix.