Like LessPop_MoreFizz mentioned, the only way to normally prevent the infame hits is to do the add-on before starting the Things that go Boom and Render unto Caesar quests. The only way to prevent the infame reset triggers is thus to not enter the lucky 38 or the tops casino before finishing the add-on.
To reset the infamy of the factions use the following console commands:
For the NCR use:
setreputation 1 000f43de 0
For the Legion use:
setreputation 1 000f43dd 0
This keeps your normal fame, it just makes them forget all the bad stuff you did.
I think that simply removing the don't tread on the bear quest is not enough. When this quest is failed certain NCR NPC's dissappear from the game. I think you need to reset the quest status back to phase one, and enable the NPC's again.
Try this to reset the quest:
setstage 00167f0e 1
And use these commands to enable the two NPC's (replace refID with 00116840 (Crocker), and 001206fe (Moore):
(For the best effect stand at the position the NPC would normally appear).
Not 100% sure this is all you need to do, the don't tread on the bear quest might set some more variables that you need to reset yourself, look at the quest console commands and try a few of those.