Alright, I'll look into it here and keep you all updated

Thanks for looking at it!
Edit: It helped a lot, but unfortunately, didn't solve the problem entirely. Welding the vessel then running the STL check showed the problem faces - a quick Cap Holes and applying an invisible texture fixed all the STL errors. The smoothing worked well, but there are still areas where you can fly through the ship and you can fly through the antennas almost completely. I think this may have to do with the BSP data being generated from the smoothgroups over such a large area with such a low-poly mesh.
Looks like most of the lighting will be ambient then, to cut down on the glare of the models since there's no way to make them smooth without breaking their collision, even if the STL check returns no holes or other errors in the model
