My intention was to do a few jobs for Ceaser & then stick with the NCR. All in the sudden I now have a "Merciful Thug" reputation with NCR. I've tried everything I can think of to raise this back up including console commands however now I have RANDOM NCR troops killing me on site no matter what. Any thoughts on how to fix this so the NCR does not randomly shoot me on sight, my current reputation is "liked"?

I'm not entirely sure, but I don't think you should be getting attacked if your reputation is "liked". Are you wearing Legion armor?

Nope NCR armor & the second I take it off ALL of NCR comes after me. It's like the game is in some kind of perpetual loop that has NCR AGAINST me?

If you haven't been to the Lucky 38 yet go now!!!

to late... =(

It could be because you're pretty much doing the same quests (with some exceptions) for each faction, just on a different side.