I think it helps in the early years to reduce the active roster limit. There simply aren't enough historical players to support a 25-man active roster in 1901. Try knocking it back to 22 or even 20.
For what's it worth, historically speaking, the active roster limit from 1901-1908 was only about 15-16. The 25-man figure wasn't established until 1909, and even then it was reduced to 21 or 22 in some later years.
Check out
this page from
this web site for a table detailing how the roster limts have varied over the years. There's quite a bit of interesting stuff on that site, it's definitely worth checking out.