Well, I spent last night reading the manual and noticed the EGR valve has two air hoses to it, one on top and one on the neck (tube), when I did my testing I only removed the one on the neck, when I remove the hose on the top it runs 90% better with only an occasional miss, so I am going to replace the EGR valve, the weird thing is I cleaned it out real good and tested it it when I had the motor apart, and it seemed good, I am going to order one from the dealer unless someone can recommend a better aftermarket EGR.
Also, would it hurt driving the truck with the top EGR hose disconnected?
Thanks to the guys that offered advise