Okay, I posted all my bug reports very VERY tired at local time of late in the night.. so excuse the bad grammar and lack of editing and saves.
I've gone through all my "this thing crashes" saves and the vault city error apparently vanished on its own, I'm thinking it had something to do with a restart of my system. Tho i have no idea why that would affect anything, anyway, cant reproduce the bug anymore.
The part eating gecko reactor was apparently already fixed, thanks for doing that!
The slag bug is clearly just a misaligned trigger for the conversation, there appears to be 2 different paths to start the first conversation (fall through trap, or visit at night and talk to the guy at the gate), if you first fall through the trap, then go through the 1st quest and then the next time you visit you talk to the guard at the gate vegir doesn't check if you've already talked with him once, he will just re-initiate the first time dialogue. There needs to be some kind of check on "have met = Yes" on the first time dialogue or something. If save is required i can email it to killap.
The Klamath combat thing is pretty likely a misaligned hostility check or something. It goes like this:
Talk to duntons about them hassling torr, threathen them, duntons attack. Everyone in bar stays neutral. But if you run to the door and fortify it so its only 1 dunton at a time and one of the kids happens to be within an earshot. The kid will start to throw rocks at you, while no one else turns hostile. Once both duntons die the kid will remain hostile until you leave the combat area and re-enter. Once you re-enter they are all friendly. But if you kick the kid and drive him away without killing, then the rest of the town turns slowly hostile, tho not all at once, for example i could end combat and sit next to sulik (not hired at that time) for 5-15 seconds then he at random turns hostile. I think this has to do with not setting all klamath neutral on the dunton VS player fight, just the people in the bar. As with previous bug can email save if Killap wants.