1. Not sure on the ECUs. Might be easiest to keep the ECU w/ the engine it came with.
2. My first time pulling one of these but it's pretty straight forward. 2nd set of hands will make it easier when undoing the torque converter bolts. Can leave the hood, just undo the struts and tie the hood up higher. The trans oil cooler lines are the only tricky things I've found so far. Undo the harness at the ECU and bring the loom through the firewall. Can leave the compressor lines connected and lay it down. Or disconnect the lines, pull the compressor with the motor and re-charge once back in.
I'm about ready to lift the motor out on mine for a full re-seal. Sounds like you're going to do all the engine related seals, rear main, oil pump o ring on front and the same o ring on the rear of the motor? Check motor mounts. Great time for new radiator if needed. Fan bracket too. Mission creep can turn to mission sprawl when pulling the motor....
Good time to address any issues with steering rack or the front diff as well. I'm swapping in a new rack and doing all the diff seals and bushings at the same time.
Good luck!