Mods working fine... I used FNVEdit to make a master as TESsnip was not working properly, everything mechanically seems to be less glitchy. No duplicate or misplaced objects or conflicts. Just one little thing: I got this message in red text "WARNING: This plugin has the file extension .esp, but its file header marks it as an esm!". It's making me feel leery as it seems so ominous, does this mean somethings wrong/that the mod isn't yet ready to be publicly released at the Nexus, or is it just slightly alarming red text that can safely be ignored? Did I do something wrong?

http://imageshack.us/f/807/problemj.png/

^ Screenshot for context

The game engine doesn't read the file extension to determine what's an ESP and ESM, but the flag you switched with xEdit. It's not as scary dangerous as you think. It'll just be mis-ordered in pretty much any load order editor besides FOMM, since it seems only FOMM considers the ESM flag in ordering.

You should be able to change the flag in FNVEdit, every file has its file header displayed and you can edit it.

I'm no expert, but it does this to every mod you have loaded when you do a "master update" with FNVEdit. If you want to remove some mods or whatever you have to do a "master restore", which removes that message.