@Ultra123
There is a limit to the number of factions that can be made playable at one time in the beginning of the descr_strat.txt file. If you make a faction playable, you have to make anthother, previously playable faction, unplayable. This can be changed by the user on a campaign by campaign basis if desired. I don't know if this is your problem, or if you have already addressed it, but it was the first thing that came to me.
It looks very good so far.
Have you deleted the map.rwm file before starting a campaign?
I noticed that in HHB, the provinces that the Mongols start with are listed as owned by Russia in the descr_regions.txt file.
I found this code in the descr_stat.txt file and I think it may be your answer.
It appears to me that this is where the ownership of the settlement is assigned.