Edit: It's part VI not part V, sorry!

Ok so I'm about 40 hours in here and I just completed the Brotherhood quest for Mr. House (Downloaded the mod which reactivates the diplomatic speech check to not kill them). Now I have to go save Kimball at the Dam, but whenever I go there the NCR are hostile (except when I have NCR armor on but I refuse to wear it for the rest of the game just to avoid this), likewise for every single other NCR location in the game, they always shoot at me.

I have already done Crocker's quests so I can't get the pardon I've heard about from him, and he is also hostile if I revisit him and change armors.

Before deciding to do Houses' quests I started doing Yes man's side quest to contact people and completed it. My theory is that the negative reputation gained from that plus Mr. Houses' quest line have combined to lower me from neutral reputation to Wild Child. Is this possible? I should mention that previous to this I was at I believe maximum positive reputation with the NCR at idolized. Also before going anywhere with NCR my rep shows as "Neutral" on map locations until the NCR attack me and I respond at which point I lose karma and end up at Wild Child :S

Oh and also although you probably guessed I failed the Don't Tread on the Bear! quest.

Is there a way to fix this? Let me know if theres any other information I need to give.

Thanks in advance.

If you've failed Don't Tread on the Bear, then the NCR will be permanently hostile to you for the remainder of that character's career because you're working against their interests. There is no way to fix this except using console commands to rejigger your reputation, but I would advise against doing that since backing one of the factions is supposed to make the others hostile.

The problem is that the NCR aren't supposed to be hostile here at all. The objective of Mr. Houses' quest is to go to Hoover Dam and help save Kimball, which I presume means the NCR are supposed to be neutral or something? If doing some of Yes Man's quests before changing your mind and doing Mr. Houses' causes permanent NCR hostilities then there really should be either ways of preventing it or a way to fix it because it makes it impossible to continue without wearing NCR armor which strikes me as incredibly silly.

The way Don't Tread on the Bear and Beware the Wrath of Caesar work is that when you fail them a large negative hit is applied to your current reputation with the faction in question. If you haven't done anything for them then odds are good that said hit pushed you into permanent hostility status.

Progressing to the point of the Kimball mission will make you permanently hostile to the factions you did not back (save Yes Man, who doesn't care), because at that point you are locked into your faction choice and the others will not work with you or in many cases even talk to you. FWIW, the last time I did a House run I did not need an NCR outfit to save Kimball; a recent patch changed how getting high positive or negative reputation works, however, so the hit may now be too big for Neutral status to be sufficient to prevent permanent hostility. It makes sense that you would need to appear to be a member of the NCR to get to where Kimball is, since they have good reasons for keeping potential hostiles away from him and you happen to fit that category, so disguising yourself as one of them allays their suspicions long enough for you to get in, do your thing, and get out.

You are correct, though, that the NCR is supposed to be Neutral towards you when you start this quest, so the additional hit from the Yes Man work may have been what pushed them over the edge into Hostile. The Yes Man route is at least partially meant as a 'safety valve' in case you managed to piss off the other three by mistake, so it's set up to be workable alongside one of the other three factions' tasks; since people usually pick a side ahead of time and run with it this is rarely an issue, as they won't be doing the Yes Man tasks, but if you switch in the middle you retain any reputation hits from the other faction's work and those stack with the hit from the special NCR and CL rep quests. In your case the cumulative hits seem to have pushed you into permanent hostility with the NCR, and I don't know of any way to fix it short of going back and doing either House or Yes Man, but not both.