I see one problem (this is more like Fs2 than Fs1), there is hardcoded limit of weapon types per ship that is set to 3 types (I guess that rest od them have to be set as ship "abilities/special attack").
Danman wrote a pietition for developers to release those hardcoded limits, but it would be anywhere soon coz it require to re-write the game engine
HOWEVER I think that it wouldn't be a problem for Fs1 capships as GTA and PVN use 3 types of capship weapons max (excluding Aten cruiser which has a werd config that use two fighter weapon turret - but they can be replace by capship turrets)
GTA/PVN capship weapons:
-terran/Vasudan Huge turret
-(terran only) Fusion mortar
-(terran only) Fighter killer
Shivan on the other side have more of them:
-Shivan Huge turret
-Shivan Mega turret
-Shivan cluster missile (anti fighter weapon)
and I'm afraid that SD Lucifer has all of these types on board.