I used FOMM's BOSS Auto Sort feature to rearrange my mods and didn't back up the previous load order despite the warning. It was extremely stupid, I know. Now there are red triangles with exclamation points everywhere, load screens don't appear, weapon sounds don't play, etc. If anyone can pinpoint what the problem is in my load order, that would be amazing.
Here is my load order:
FalloutNV.esm
Advanced Recon Tech.esm
AWorldofPain(Low Loot).esm
decwithreg.esm
CFWNV.esm
IWSCore.esm
MorePerks.esm
OWNB -OpenWorld.esm
RZW_Master.esm
RZW_Television.esm
DSWH40K.esm
Tales from the Burning Sands.esm
wsix.esm
MikotoBeauty.esm
Primary Needs HUD.esm
Nevada Skies.esp
Fellout.esp
WeaponModsixpanded.esp
RustTownV1.esp

Have you tried using wryebash? Create a bashed patch file. At the very least it would be a very simple way of checking to make sure your master files are ordered right. It'd also give you an error messages that might be helpful(If it really is a mod being out of order).

No, I haven't used wryebash. Where can I download it? The only place I can see where it's available is The Elder Scrolls Nexus. Will it work for Fallout: New Vegas as well?

Slightly different name, for the new vegas version here is the link

http://www.newvegasnexus.com/downloads/file.php?id=35003

If you use boss, not sure about the fomm integrated one, but the stand alone also gives you a html page with recommendations on what settings to use for the patch. If the built in boss you used doesn't do that, I'd recommend going for the stand alone boss.

Will you tell me how to create a bashed patch file and how to install Wrye Flash correctly? I have no idea what I'm doing and can't seem to find any good tutorials anywhere.