glad to hear that you enjoyed the game.
Regarding Serafine, you can give her a milkshake that will increase her favourite points.
concerning the automatic ship maintenance, I might add that capability to khelara once her tech skill is high enough
As to the other issues:
Never use any mods our third party program, they will screw up the game call hierarchy, data and other things. Also do not edit characters attributes/stats on command line, those are triggers for some quests that might not ever come otherwise. These are some technical limitations I cannot fix unfortunately.