Canyon, I would do exactly what your doing. I would never install the 360 without doing the things I planned. Harder to do it in the car, and no need to put it in, only to pull it out and put it back in again. I would put a new rear main seal in it, and while the pan is off inspect the main/rod bearings. I would pop in new freeze plugs. I would install a new timing chain with the cam. Nothing I mentioned here is hard or expensive, and easily done with the motor out of the car.
If your interested in some head work, I have a thread with a "home port" video posted right now. I would suggest if you did the heads, cut them .040 to help compression a little.
The rear end will change out the same with or without the 360 in there. I've beat a while on several 7.25 rear ends before upgrading, and I've never broke one.