Fixes for Ferguson's Mechanical Paradox Replica Thingiverse #93418

The attached files are replacement top, bottom and connection pieces for the project described below.
I've been spending time with various gear design and testing and came upon the Ferguson's Mechanical Paradox Replica by sawdusty posted May 24, 2013. He stated that he had not printed the design and that he didn't know if it would work. The project was appealing, so I decided to try making it. I printed the parts as shown in the photos and found several issues:
1) The size of the h