Jeff, a lot of different questions seem to present themselves there.
I'm a mechanicals guy. If the car doesn't work the way it should, it doesn't really matter what it looks like.
I'm a fan of completely going over the underpinnings. Anything that you're re-using from the pan should (IMHO) be cleaned, primed and painted before installation. While the body's still off the car is your best opportunity to do that.
It'll forstall major work for a few years if you're able to confidently clean everything up. Put the body on a trailer when you're about ready to put it on the car -- take it to a painter, get the best paint job you can afford when you get to that point, and confidently park it on top of the chassis.
I think you'll be a lot happier than if you're monkeying around with chassis pieces later in the game.
You'll want to put the body on for a test-fitting and adjustments anyway, so you might as well not worry about dings while you're doing it.
Measure twice, cut once.
Merklin will be along shortly. He's done about a million of these things; I'd say he'll probably be the expert opinion ...