It was definitely the respawn mod. Every single region except for some islands had a maskling camp, which was causing the problems. I made a new game and have built more than a dozen interconnected cities without any trouble. For now I've made a slower version of the mod (15 years) and will just manually turn it off periodically.
That said, outside of a few minor issues, the recent update feels amazing. Great job with the new map generation, the mountains and rivers look and feel better and the tin balance has been great. Sea trade has really opened up options for expansion and the UI changes feel really good. I know there is a lot more you plan to do and I can't wait to see it. Great job!