You may have multiple issues.
First, what thermostat did you put in it (temperature setting)?
Do you have a buzzing noise from the "speaker grill" above the driver seat? That is one of your cab temperature sensor (I believe there is a second one in the rear in the headliner). If it is buzzing, replace it.
Second, before you replace more parts, do a fuse pull reset (there is a proceedure floating around here that explains it). Pay aytention to the actuators to listen for them moving. If you do not hear them cycle from floor to defrost during the reset, then check the actuators.
Do you have the mirror with the temperature display? I could be wrong (if I am, please correct me), but I am pretty sure that in auto, it uses that number (outside ambient temperature) to add or remove outside air as part of its temperature regulation. I have read that replacing that mirror has fixed similar problems, but not always (it is a bit on the pricey side). Side note, while I have read that the outside ambient temperature sensor in the grill rarely fails and should not be replaced, it is a cheap part and simple to swap out (it's outside your radiator to the right of the transmission cooler I believe). I would change it just to eliminate it as a point of failure (Actually, I did while troubleshooting my '03.).
Lastly, the climate control unit itself has been known to fail, but again it is an expensive part, so if anyone has a way to verify it is working properly, please chime in.
I hope some of this helped.
