One is obvious, he is flying. His feet aren't touching the ground.

"Can't you just lower the model?"
Sure! If I knew how... but I don't.
The second problem, is he needs his hand bone labeled so the weapon will appear.
Third... but not really a "problem" is he's actually holding a sword that just disappears in game... don't know why, didn't matter, I'd delete it anyway (if I knew how).
Here are the source files. Any help is very much appreciated.
http://z.nexuizninjaz.com/models/nxmdl-ninja_test.pk3