The "rectangular holes" in the engine block look to be locators for the motor mounts.
What I'm noticing is a duplication of parts on a few trees indicating possible different versions / issues of this kit. I.E. the interior sides with duplicate radiator hoses and radiators.
The two "frame" trees both include parts to build two complete frames, cross members and all.
What is the large rectangle piece at the bottom right on the "wheel" tree? A top insert for a coupe?