Okay. The bolt holes were about 1/4 too high when I installed the unit. I measured old vs new and there was about 1/4 difference, too, from the foam edge to the bolt holes. So I hacked 1/4" of foam off of the bottom of the new unit. Upon installing it I noticed the drain tube was what was causing it to sit to high. The new unit didn't have a provision for the tube. Oops. I need to seal the bottom with spray foam now.
One of the tubes is jammed up against the feed for the propane burner. But, looking at the old one the paint is all banged up in the same area so it must just be that tight.
Pics:


I need to reinstall the chimney and other random sheet metal, but I'm getting close!