I was wondering how do you split appart a connected mesh (Like taking the mask from a flame atronach or taking away just one gauntlet from an armor set)?

Blender + basic understanding of blender + newest Blender Nifscript to import & export your work directly as .NIFs + some brainzzz. That should do it.

You can do limited splitting in nifskope, but only on objects which are already made up of different NiTriStrips (parts).

Get Blender then get http://cs.elderscrolls.com/constwiki/index.php/Custom_Cuirass_in_Blender_Part_1 if you aren't familiar with it. What I do is, have you project open, say a cuirass; then you import, for example, the elven cuirass because you want the paulderons. After it's imported you clip away or delete what you don't want. When it is exported it becomes one file. I like changing the textures with http://sourceforge.net/projects/niftools/files/. Anyway I find it's a lot of fun chopping and cropping armor meshes.

Elora Q

Enter edit mode "A", activate your area (vertices, edges or faces) and press "P".