Hope I'm not intervening here but I thought I might offer my 20 bux on the polygon issue.
I can think of only 2 common problems:
-From the looks of things, somewhere in the conversion process, it's getting set to 'double sided'. To check for that, zoom to inside the model and if you can't see anything but polygons, then that's the case (Normal one sided meshes would look invisible from the inside). There should be a setting in 3dx that lets you change to/from double sided.
-Either that's the case or when you mirrored the pylon/nacelles, you also mirrored the entire ship with it. The only swift way to fix that is to start over from the original and hope it doesn't happen again.