is this an obd2 truck? (96+) If it is an OBD2 truck, does it have an o2 simulator for the cat-mouned o2 sensor? (keeps the computer happy)
How's the plugs look? Is it getting good fuel and spark? Most modern engines with the restrictive (quiet) induction and exhaust systems sound like a retarded vaccum cleaner anyway. It sucks. Check vaccum and see what that reads. If it's tuned up right and stuff, check compression in each cylinder.