To reset the infamy of the factions use the following [console commands][console]:

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][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):

    prid refID
    disable
    enable
    kill 
    resurrect
    moveto player

(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][quest] and try a few of those.

[console]: http://www.falloutwiki.com/Fallout:_New_Vegas_console_commands
[bear]:http://www.falloutwiki.com/Don%27t_Tread_on_the_Bear
[quest]:http://www.falloutwiki.com/Gamebryo_console_commands#Quests