So my truck is not making the usual 40 pounds of boost pressure, the exhaust temps are higher normal, hanging around 900 degrees F, typically they this never gets above 800 degrees F. In addition, my fuel mileage is way way down.
Could the above be caused by a clogged charge air cooler? If the air cooler was clogged, wouldn't the truck over heat?

 

sounds like you have a boost leak. most commonly on the 12valve trucks it is the boot where the charge piping goes into the intercooler. there is a sharp edge from the inner fender and over time and as the boot stretches when you apply higher than stock boost pressures, it will rub on it and cut it. check all the boot connections from the turbo to the intake horn and I bet you will find your problem.