I'd like to be able to help you more but I'm just a beginner. So the only thing I can do for now is to give you some additional feedback.
However, you may want to take a look at the Darth Revan mod
which turns the PC into a Jedi on the Endar Spire. I've been using this mod during a few games and never ran into any problem.
Things that work fine with your editor:
-I changed the skills, name , attributes and feats of my PC with your editor while using the Darth Revan Mod and everything was ok.
It seems that the problem only arises when making a class and gender change.