Owch. This is why I refuse to just "fix the one issue" and bolt it back up. I always at bare minimum replace all clutches, inspect, and replace all solenoids. All solenoids are something like $80 so it's cheap insurance against having to rebuild it down the road. At that point, an entire master rebuilt kit is only $500 including the solenoids, so I almost never do a partial rebuild for this exact reason.
Glad to hear they are taking care of it though. I know installing these transmissions are a pita so I feel your pain having to pull it again. At least you can save money there!
