First off, tell me from which prog did you port the model back to nif (and if you backported the ship from nif in the first place).
Second, in the HP find the damage resolution of the ship and make it 1 or less, MPE gives a default of 10 which is waaaaaaay too much for any ship.
Secondly, the weapon damage resolutions need to be below 0.1 too for all weapon types (higher is just too much - I have it at 0.06 for the Novi Sad refit I'll release soon).
This way, you wouldn't be able to destroy the physical model without destroying the ship itself which happens with sooo much ships (so no transparent ship crap).
Also, in the py in scripts/ships look at the part digits where the glow and specular suffixes are set, and find something what works nice (the LOD (Level Of Detail) part should be getting bigger with each LOD type (low, med high).