why are you posting an OBJ file for an animated gun?
OBJ is incompatible with FPSC, and contains no animation data.
Your transparency issue is odd. doesn't look like the faces are flipped, but more like the texture it'self is wrong...
I know you use maya, so heres a quick hint for the UV maps. Geting them on one map (as opposed to multiple.)
Select each part of the model, and go to "window"- UV texture window
leave that open as a floating window and return to the mesh viewer, now select each mesh in turn, and when it appears in the texture viewer, rightclick and select "UVs" from the selection menu. Move the UV outside the positive (top right) area of the graph on the UV editor window. DO this for all your mesh components. you should now have all the bits of your UV map outside the UV map area, choose select all, and select all of the meshes, switch to UV map window, and you should be able to see all the meshes maps. now you can go about placing them all in one texture file!
Anyway, nice model, you've come a helluva way!
Butters