I figured out, or at least have guessed what is causing the bug.
When you do the quest "Bust the Skulz" there are two options for quest completion, a violent one and a non violent one. The violent one goes like this:
Talk to the gang leader
Steal the Urn
Talk to the gang leaser
Either agree to kill the bartender or turn them in to Lars and kill them with the help of the guards.
You will take a Kharma hit for stealing the urn and get a massive Kharma boost for returning it should you side against the gang (net win).
The peaceful one goes like this:
Talk to the girl who hangs out with the Skulz
convince her to leave the skulz
wait a day
convince her to turn evidence against them
Tell Lars she will testify and they are all peaceably arrested.
If you start the violent one and then resolve it peacefully, you will get a crash as the violent one can no longer be completed. I stole the urn, then got the the girl to testify against them and when I went back to turn in the urn for the Kharma reward it crashes EVERY TIME. I can enter the northernmost quadrant (with the casino and the Scum Pit) by exiting to the world map to the south and then selecting the area to the north to re-enter but it WILL crash in a few seconds or when I approach the bar. I have ONE save game from before entering junktown, when I got Tandi (and she never went home again, lol) so I'm considering either loading that or just starting over. Loading that game and testing it out however confirmed that his causes that glitch.
Meanwhile, since I won't be playing that char I headed down to the cathedral and took on The Master; I don't think I've NOT used the Brotherhood disk +speech +science checks on him before (except that one time I set off the bomb) so actually fighting him was something different. I used the Followers to good measure, arming them with rippers and super sledges and through trial and error I found out The Master wont shoot his chainguns it he can't see The Vault Dweller so I stayed back behind the pillar, picking off the mutants he spawns and letting the NPC's fight the Master until I was ahead of the spawns and could pop out and get a shot on The Master and duck away. Nobody would have died if Cassidy, errr, Tycho hadn't been "oops!" shooting people in the back the entire fight but all the recruitable NPC's and one of the sledge wielding black dudes (he was knocking down nightkin left and right) made it out.
