Nice pictures! It looks like even though two levels of plumbing make it more complicated, the designer has everything laid out very straight and proper.
With an elbow in the 3" drain and some space to work with, it will work in your favor to relocate the toilet. If the 3" through tank fitting is a pipe-through-grommet instead of a solvent weld, you should be able to just spin the 3" entry to fit your needs.
Following along to see your progress, this is really a rig worth the effort and it will be cool to see what you end up with.