Crit and Uber already work differently from normal Mannpower runes.
Crit respawned evey 60 seconds and lasted 30 seconds.
Uber respawned every 180 seconds and lasted 30 seconds.
Having said that, I think Valve largely removed those two powerups in favor of the Revenge powerup, which is a Crit powerup that only spawned if the the game was "significantly unbalanced" meaning that the other team had a significantly greater percentage of the normal runes than your team did.
Not that the last part would matter if you're putting them in MvM.
Useless Side note: In MannPower mode, the actual runes are item_powerup_rune and item_powerup_rune_temp (for Uber/Crit), but there is no way to directly set the rune types as it's not an exposed property. Instead, you had to use item_powerup_crit, item_powerup_uber, and info_powerup_spawn points to spawn them.