Would it be possible to just make it so every challenge completion gives you 5 gears no matter how well you do? That would probably fix the having to reactivate the mod cheat every time you start the game, and it would somewhat maintain progression too.
You might not be doing something correctly as the mods don't reset. Granted they don't show "green" but if you mouse over you will see active/inactive. After my initial setup, having some disabled some enabled, I have not had to redo any mods even after pc reboots. Just hit option "zero" and everything turns back on right where you had it before.