1. End the season and save the roster.
2. Exit the game and run the Toolkit.
3. Un-tweak the ratings of the saved roster using the MegaModifier. I.e., if the tweak is FG*0.6, then do FG/0.6.
4. Run the game and play the off-season.
5. When season starts, save the roster. Exit the game and run the Toolkit.
6. Apply the tweaks using the MegaModifier.
You're done.