The way around the player / npc ship problems is to script two ships eg: npc_shipname & ply_shipname.
I left the vanilla ship as they were for npc then replicated a set for players, it is a bit of work to alter and add to files but makes life a lot easier, for instance loot_drop. Also this gives you a chance to fix up some of the issues in ship arch and add npc only ships for players like Capital and Transport ships