After resigning to the fact that there is no magic that will make STL files real, I sat down to suck it up and assemble the STL files with insanely mated hardware, when I did have one more thought. It seems Inventor is able to create real surfaces from hole geometry in STL files. If the surfaces could be exported along with part mesh in an IGES or STEP format, these new parts could be brought into Solidworks and used to create a decent assembly by mating hardware to the real surfaces then hiding them, albeit with a bunch of ugly mesh lines.
So I gave it a shot. Loaded up a corner block and created surfaces from the holes, then tried to export. No dice. Tried every format. Nothing. Then remembered the mesh converter for inventor and installed it, thinking that I could convert the STL to mesh that would export along with the surfaces. Seems I can’t get the option to convert mesh to base feature yet in the right click menu. This was very late last night, and I was shot, so maybe tonight I can get the mesh plugin to work and make this happen.