I wanted to pop in here and say, after basically giving up on this problem for months, writing it off as a lost cause, I just on a whim ran the game as administrator today, decided to try out one of the scenes that had previously caused the crash...
Ran the scene 3 times, no problem.
Assuming this holds, I am almost annoyed by how simple that was to fix.
Still, thank you for all your help, and for the great game.