Didn't realize working for the Legion would make the NCR hate me, making me hated in many towns and making things plain annoying. I'd rather work for the NCR.

Is there anyway to get my fame back with them or am I in too deep?

Once you fail the NCR quest that warns you "continuing helping Legion will make NCR hate you" you are screwed. There is no turning back. You are now locked into Legion (and possibly Yes Man) track.

You can use NCR Faction Armor moving around NCR lands (just like you can use Legion Uniform to move in Legion lands)

Weird thing is the Legion attacks me outside their land even though I'm working for and am on good terms with Caesar, just as the NCR does. Must be a bug because I enter and leave the fort / their land freely.

Certain companions attack the Legion on sight, regardless of your affiliation. You traveling with anyone?