Hello and welcome!
I am really sorry I don't have an answer for you but I didn't want to think you were being ignored! I hope someone here does have help for you! Glad to have you here, post us some pictures of your truck!
I just found this on the net:
The P0406 sets when the EGR position sensor's signal return is the same as or higher then reference voltage. Without doing the actual tests on the circuit; I would say that the EGR position sensor is likely at fault. Ive had to replace a number of valve/sensor assemblies for this reason.
As for an extended emissions warranty, call the dealer with your VIN # and mileage and theyll tell you whether there is any coverage for this.
Maybe this will help?