Re-torque your cross tubes, 39 ft lbs. If you have a 24mm and a 19mm crowsfoot for your torque wrench it will make the procedure easier. If your tubes are loose, you lose rail pressure, hence the long crank times, also could be causing the idle issues.

Remove the intake horn and injector lines for access, not too bad a job, about 2 hrs start to finish.

 

I guess I need to get this thing hooked to a good computer as a next step, a friend of mine has a very new updated Snap-On one.

 

Give this a try AAPPS 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
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


blacksmoke

 

Have you done this on your 04'? I will have to give it a try, anything is worth a shot.