I'm hoping that it was the "new" pump they put in. As for them replacing the already replaced pump, is beyond me. I've heard horror stories of dealerships not putting oil in, and I didn't check. I was more concerned about getting back to work unfortunately and didn't even think about it.
Would a failing pump explain it shifting to third, then not shifting anymore?
They replaced the pump, and did another reflash "ecu upgrade" on it (the service desks exact words).