So the whole time I've been making my mod the faces on my NPC's were grey, I thought that maybe it was just the CK being wierd but when I put it in game it was still the same....any tips? Any advice would be helpful!

This one has been around for a while. See the http://www.creationkit.com/Dark_Face_Bug on how to get around it.

You don't need to 'esmify' the mod at all. Just select your custom NPC's in the actor section and hit Control+F4 and click Yes.

And it's not a bug, it just works differently than it did in past games.

I agree with AJ, you don't need to "esmify" the mod. It works fine with an esp. You do need to be sure there are no face or body mods active. There should be no external meshes or textures affecting the actors. Load your mod and find and select the actor or actors in the object window. Hit ctrl-F4 and you should get a dialogue asking if you want to export texures for the selected actors and respond yes. It will set up the appropriate folders and files that need to be in place to fix the faces. You can then reinstall any face and body mods you want to use. If you make any revisions to a face in the CK, you need to export them again or they will be grey again. Those meshes and textures need to be in the folders they are set up in for every user that has your mod so they must be packaged with the mod whether loose or in a bsa.