About Historical League injuried player
 

I'm going to set it to 1999 and then proceed with the game.

However, players who were injured or suspended that year, such as Kerry Wood and Matt Morris, remain free as FA.

I set it to Career Mode, is there any way I can get these players to go back to the team (so that injuries apply)?

This only happens to players that missed the entire season.

There isn't a one-step fix for this, but you can assign the obvious ones back to their correct teams and give them injuries using the editor.

If you are using Real Transactions, they will stay in the free agent pool and get assigned back to their teams when you move the the next off-season.

Also players who were in the minors that year but MLB before will be FAs when you import full history. The quick fix for this is to use full minors.