Mission creep is setting in...you're just one or two rationalizations away from pulling the engine and stripping the car to the subframe. I think you should just go ahead and do it. Clean up the cowl and firewall, get the core support looking good, paint the subframe and suspension components....I did the Gold Car that way without pulling the front clip and it turned out great. If you ask MPR to use a sponge brush things might get ugly. BTW - your organization system looks great. Good idea.
On the underhood finishes, tell your powdercoating guy to do the inner fenders at 50% gloss, brackets and pulley's at 60% gloss, and air cleaner at 90 % gloss. You better get an AMK catalog so you can order a bunch of new tinnerman's and bolts.