Thanks for the kind words, glad this thread is helpful
The rear door gap on my driver's side is still fairly inconsistent, so no I'd say the body hasn't done much conforming. It sounds to me like your issue is more related to front clip position than body mounts. Before messing with the mounts I'd unbolt the front end supports at the frame horns and use a floor jack to raise the right front corner a little bit to see if the door gap improves.
As for the POR prep, I just use elbow grease and sand paper. Once any loose bits are removed I use their "Metal Reay" phosphoric acid mix per instructions and then brush on the POR with the cheap foam brushes from Ace hardware.