You have a couple of things you can do.
1) In you League Settings there is an option to "Allow incomplete rosters" aka Ghost Players. This will allow you to sim forward even if your rosyers are not full.
Go here:
Out of the Park Baseball Manual
About 2/3 of the way down under Player Options it explains it.
2) Once you can sim forward you can offer free agents minor league contracts to fill the team.
That will solve the problem for you.
Good luck,
Tom