Thanks for the kind words. The good news is that all you need is a custom site set and then all of the other parts of the code (such as AutoMPO, MPO, DMRG) should just automatically work. I recently made a site set for a student who is doing a two-leg ladder setup like you suggested where each leg has a different type of quantum number. If you email me I can send you the source code for this site set for you to use as an example.
To deal with fermions specifically, things might get a bit tricky with AutoMPO. We'd probably have to talk about how to deal with it best. But I think it could work ok. Basically you'd have to define a fermion string operator called "F" for both fermion and boson sites, and just define it to be a trivial identity operator for the fermion sites.
Ultimately this would be a good type of SiteSet to add to ITensor.