Brennan H,
I can't answer the first question, but here's a stab at 2 and 3.
Regarding the quantity of powder, I'd ask the guy who's doing it for you. He should have a better answer than anybody on here, since he's used to his equipment and setup. For color, couldn't he match the original paint codes, or samples?
Regarding rubber and other parts deteriorating during baking: If you are sure you'll have to replace it, why not take it off before starting the powdercoating? I'd have everything apart in individual pieces if I was powdercoating it, then put it together with fresh/new/coated fasteners and new gaskets, seals, etc. That way, the coating covers everything it's supposed to, with no bare spots from hiding under old stuff. I'd also mask tapped holes and parts that shouldn't be coated, like keeping good bare spots for anyplace you'll need a battery ground.
JMO