So I created a custom mesh and texture (both of work fine in blender 2.62) and all is good. But when I export it (as a .obj) and import it to Nifskope the UV maps are all over the place. I'm not entirely sure what the issue is but I'd be happy to see if there's a fix.

Nifskope has known problems when trying to import .obj files.

So what do you recommend?

This should help you out, http://niftools.sourceforge.net/wiki/Blender