Hello, this is a known issue we're currently investigating.
@Digijustin you are correct in that it is hardcoded to use the MLS, so if you edit the MLS instead, it should work.
Another thing worth noting is that the MLS is required to have 24 teams in order for the North American continental cups to run.
In your original file, changing the rules to affect the MLS and then increasing to 24 teams should allow the cups to run.