I'll add on to this and say i know how to start odd team seasons with odd # of teams.
1: Do the first steps in BaseballMan's OP above. (Do NOT balance the leagues in Teams.csv)
2: Create a Fictional League starting in 1871. (or the year of your choosing)
3: Go into Commissioner Mode, and delete the league in Game Setup > League Setup.
4: Go to the Free Agents Screen, and Delete All Free Agents.
5: Go back to League Setup, and click Add League.
6: Click Create Historical League, and create the league of the year you want.
7: Your league should now be created and should look something like this:
Have Fun!