Well, I wandered around in Upper Avernum for a bit, and two new things happened:
The important Vahnatai (I don't remember his name) let me talk to him about the surface plagues. I told him about the slimes, the cockroaches, and the golems (Nothing came up about the troglos/giants). Even though I had defeated all three, it only let me tell him that I had completed the slime plague.
The second thing that happened was that the golems at Erika's tower let me pass. I guess my reputation got high enough (It's at 60).
I remember that in the character editor, it has the "Set Stuff Done Flag" tool. Would that help me at all? I have no idea how to use it.
EDIT: I did get into the bunker in New Cotra.