*Disclaimer...In no way do I suggest this will work for everyone, nor is it even feasible in some cases, so sorry if you find my suggestion preposterous*
I think I was able to resolve this over the weekend by essentially resetting my world. Here were the steps I took:
1. Made a backup

2. Released all players in all leagues to the FA pool
3. Deleted all FA's and Retired players
4. Erased league history
5. created a template of my world structure
6. Created a new fictional league, using the template
7. Filled teams with fictional players
spot checked some of the countries that were messed up before and they are now correct. looked at about 25 teams over all of the leagues and confirmed they have correct city/country pairs. Yes, I had to lose my world that had 100 years of history that I simmed in OOTP11...but oh well.