I've got an 2003 Lightning that runs fine when I do normal driving but as soon as I get on it, it starts missing. It doesn't miss real bad to the point where it wants to cut off, it just missing a little to wear it doesn't have the power it use to. Again it only does this when the super charger is kicked in.
I've taken it to a mechanic and they put it on a computer that he said costed $11k and everything came out ok. I've replaced the fuel filters, the O2 sensors and ran serval bottles of fuel injector cleaner threw it and it still does the same stuff.
This may sound like a stupid question but what kind of fuel are you using? On a lighting you NEED to use Priemium fuel ONLY. Mid grade and regular will cause that truck to run rough in some ofthe ways you are describing.