Well, actually I have no idea what might be causing the CTD. IMO MonkWarrior has done far too much at once. After all the modding I have done I have learned the best way to progress fast is by progressing in very small steps.

I first edited the descr_strat to the bare minimum with 2 faction and 2 settlements. Then I edited the campaign map by removing regions a small batch at a time. Then move the provinces to small blocks on the side of the map so that you have the space to make a large blob that resembled Japan. Then I moved the regions back in (in small batches). Once that worked I started to edit height/boundaries/groundtypes (small changes). At lastly I added the factions back in. Since the changes were so small I could very easily pinpoint the error. And of course backup! I had 60+ backups that allowed me to return to an older version if I just couldn't find the problem. Since I only make small changes I had only lost 10-30 minutes.