I don't have time for a lot of (or, probably, any) follow-up questions, but it's more or less accepted in contemporary ontology that every solution to the problem of universals has a prima facie problem with a fundamental relation (e.g. universals and tropes and the instantiation relation, concepts and the falling under relation, etc.). It's also more or less accepted that there are ways of reducing these relations so that they become unproblematic (e.g. Armstrong's reductive principle for internal relations, intentionality, etc.).
The stuff on the "nature considered absolutely" (which as far as I know is unique to Thomism) is also relevant.