[geeper]

I am running into the same problem. We have the trunk lid mounted and we revised the latching system to use parts from the hood latch. We are now ready to drill the holes for the rear bumpers but before I drill, I am doing a LOT of measuring and rethinking.
My trunk has the same defects. The trunk floor does not run parallel with the rear frame but the placement of the rear bumper brackets appears to align correctly with the rear body. I am using aluminum shims (~ 3/8") for the back of the body.

I agree that the CMC is a partial kit of parts, considering the missing parts and extra parts they ship. I have two sets of door hinges, no steering wheel etc....
We will get this together eventually and it will be a nice car but it won't be an easy assembly. This is our second year working on it (the previous owner gave up) and we are redoing a lot of his work.