Just keep the Senate and the Rebels/Slaves as unplayable and no ill will befall you. They are both very buggy and can cause a variety of CTDs. All other factions are ok to set on playable.
If your problem persists, then check the modding you did. Make sure that the lines are as they were meant to be, that you haven't deleted eveything and that all the gaps between words are as in the original.
Good luck.
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