Replacing coils fixed the rough idle and misfire problem. But after a few days of driving now it occasionally starts slowly. It takes a few seconds of cranking to fire up. This thing is driving me crazy. I don't mind replacing the parts because I inherited the truck but come on.

 

Post some more info:

?when you put oem coils back on, do you use new boots/springs, or use old ones?

? when you cleaned TB: did you remove it, clean both sides, and use proper TB cleaner (not carb cleaner or brake cleaner)?

? Did you do throttle relearn after reinstalling?

? How old is your fuel and fuel filter ?