Ok, so what you'll want to do is go to the league menu of the Federal League once it loads in the game. Go to league settings > leagues and teams.
There you'll see a setting called 'parent league'. Change that to 'not affiliated'. Then on the 'league level' setting, change that to 'Major League'.
You'll probably have to do this each offseason as the game will want to change the league back to a minor league whenever it imports the data for the new year, but it shouldn't take long to do.
Let me know if you have any trouble.
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