hmmm... Thats gives me an idea. What if you just used the Bunker from FO1?
Modify FO1 BOS bunker to to go from the SF top level to the BOS 2nd floor.
Of course it would need to be re-populated with new critters and stuff, and i'm not sure how to tie in the Frank Horrargin killing off the BOS agent there. I mean plot wise he would now have to kill a full bunker of BOS troops, but then he did whipe out the Vault full of Deathclaws...
It woudl be interesting to expand this bunker into the FO1 bunker though I'm not sure who and what to put in there, but it coudl lead to some intersting developments.
Teh tech room where the initaite was building Power armour in FO1 could be changed into a aircraft development room, once the player gets the BOS the plans for the Vertibird parts start getting made there.
Maybe Frank kills the guy in the Den instead but the BOS dont know what has happened they only know they have lost contact with some of their smaller outposts and ask the player to investigate, when the player enters the Den BOS bunker it is now the Bunker from San Fran and the player can play the security video there to view Frank killing the BOS agent,
I like the new possiblities and quests this could add. Maybe dude_obj and Corpse coudl be convinced to add this into their expansion (Dude was already playing around with FO1 towns/maps)