Best way is to simply do this:
Code:
update npc_types set see_invis = 1, see_invis_undead = 0, see_hide = 1 where bodytype = 3;
This has already been done on PEQ, with only 39 exceptions due to being a boss/raid encounter/special NPC.
The other two are known code issues, I'm sure they will be fixed eventually.