I've got an '03 Amtran with T444E under the rear deck. One thing that I found that works really well is tractor/implement paint (I've been using Ace's Rust Stop in the rattle can). As you may have found out, the seats can be a royal pain, but press on. I'd also check under the interior steel for any potential crud in the insulation or leaks. (Personally, I'd gut everything in the interior, and start fresh)