I'm attempting to make a cockpit for the TBP Starfury. I've got a TrackIR and would like to be able to get full use out of it. I've never done any major 3D stuff before so bare with me on this. I managed to make a pit, and I managed to texture it. It's crap, but hey it suits my purposes.
I actually use this 3D program called Magic that comes with Starshatter. It's not very good, but I've used it on small mods for that game so I'm familiar with it. I finished the model, exported it as an OBJ, loaded up Lithunwrap and made sure the UV stuff looked good. I then saved it as a COB and loaded it up in TrueSpace 7.6 to adjust the scale and the way the model was facing. <whew>
SO, I then tried COB2FS2 to convert it to a POF, as well as trying PCS2. Both give me these results...on the top is the model in PCS2, on the bottom is in game:

Any ideas? Some textures aren't showing up (they are in the "maps" folder as DDS files). Originally the textures were PCX, but I converted them to DDS. Also, some polygons seem to be bleeding through. Having never really done this before I'm lost.
Sorry for the long post, this is driving me nuts.