L1ftmech,
just remember these codes will have to be cleared out of the ECM in some cases before the engine will return to normal operating mode. Otherwise the 'limp mode' will persist.
I would clear the codes... then....
if any reappear troubleshoot them and repair the problem associated with the code...
then clear them again till you get an 'all clear' no code set condition.
Then the truck should run correctly.
Note: some of these codes cannot be cleared using the pedal dance routine, they have to be cleared using the software diagnostic program.

that stage 2 overheat code has to be cleared from ECM memory once set and i definatly would find out why it was set to begin with and resolve that issue.

And yeah, sometimes you do get tech's that don't know the truck their working on and its just about impossible to get them to admit it probably because they don't want to look bad even though thier actions scream that very thing. DOH!

good luck