I just re-read your post. Every car I've ever had an experience similar to yours ended up having a bad CAT and no engine codes. I even took one car in to have the transmission checked and the transmission guy took one look at it and dropped it off at the exhaust guy across the street for me.
I know you had the CAT replaced (OEM or universal?) but it sounds to me like it's not breathing properly on the back end.
I've done this more than once, disconnect the exhaust before the CAT if you can and run it to see what happens. It won't run right but it should run better than a plugged exhaust.
