Yes when you do a mod adding a lot of factions you will inevitably get the crash involving looking at too many factions on the selection screen. There's no solution as far as I am aware.
The custom battle selection issue could be fixable if there's a way of redesigning the selection screen but again I haven't come across anyone who's done this.
It's annoying that you get some bugs you can't sort out but I'll just accept it for now. An outcome I hate as I always want to overcome these issues. If anyone knows if there is a way of sorting these then I'm all ears!