Try wrapping some tinfoil around your negative battery cable to the alternator on the passenger's side and see if that helps.
OR
Here is the APPS reset procedure:
This procedure has shown to help 24 valve ISB engines. It is basically teaching the fly by wire accelerator on these trucks to reread the position of the pedal and it's limits. Most complaints this will help with is poor acceleration, improper shifting, bucking in 5 and 6 speeds. Has been known to increase fuel mileage in some instances.
1. Set parking brake
2. Disconnect negative battery cables on both batteries
3. Turn ignition key to run(to drain any remaining capacitors)
4. Let truck sit for 30 minutes( this is the recommended minimum)
5. Return ignition to OFF position
6. Reconnect both batteries and secure, not a timed event
7. Turn key to run position(not start) and depress accelerator pedal slowly all the way to the floor
8. Allow pedal to return to top position slowly
9. Turn ignition switch OFF
10.Release parking brake
