Thank you all for your advice.
After several days of tinkering, I got several things modded. There are still quite a few things left to do.
This is what I did by editing base.charscript, and it worked fine.
I don't know offhand but might be able to help you find it, where did you find Obedient to mod?
In Potions.txt. I can use the extractor now, but I'm still not able to find the place to edit the other traits bonuses.