Ugh, so annoying. I had the right idea in the previous posts with the design of the program, but I went a little too overboard with separating the functions of the different parts of the program. Too much insulation between the parts that manipulate my resources and the parts that read files. The problem being, there's too much interconnectedness in those two fields to have separated them so much.
It appears I'm going to have to fold the application layer into the resource layer. Otherwise, in order to load a model file, I have to break away from resource handling. Which is just dumb. Yeah, a link between layers would solve it, but it's poor form. If I need the connection to be porous between the two, I shouldn't be insulating them from each other so much.
Once I have things working together, I can reevaluate if I need to split them apart to clear up things. Overcomplicating things at the outset is never a good idea.