yes a truck serial number would be helpful

but off the top of my head a couple of things come to mind here...

as edward said, insure the crank sensor is adjusted properly and the harness connecting it is not damaged in any way

also have you done a compression check on the cylinders? see if there is any difference across the board paying close attention to the no. 2 and no. 3 cylinders. its a long shot but a partially blown head-gasket may cause this symptom too.

just a couple of thoughts to ponder while scratching your head :o)

I really should ask the serial number series, but I am guessing it is an 2004, af82e,
This crank trigger wheel is where your problem is. the gap between the sensor and wheel is extremely sensitive, measure the gap in at least 4 spots in the crank's rotation to insure the gap is the same. there is a special tool to get the sensor/trigger wheel to sit just right, but my bet is that if you get it the same all the way around, it will cure your problem. you will need to loose the 4 screws/bolts that hold the wheel to the pulley until you get it within only about 3 thousandth of an inch in differences (the width of a newspaper). You will also need to use a non-magnetic feeler gauge.
also, if you have the 'PSI display' software, you will need to put this into diagnostic mode and set the timing with a timing light twisting the distributor. you should also always be sure the software is set back into run mode, and not just disconnected or the computer shut down.