Thanks for the comments. The re-tune for 4th gear really makes sense. I can also see why the guy didn't do it. I imagine it takes more time, and I was down there on a Saturday. He probably didn't want to spend anymore time with it since I'm not modded very much.
To answer another reply above, the car makes no funny noises and seems to run great. I do still have the engine light on though.
Looks like I will make an appointment with Delk Performance (recommended) and see what happens.
Thanks to all