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Did you happen to notice any fluids in the plug hole before removing them? The 5.4 is known for having coolant leak over the plugs which can cause issues as you'd imagine.
First problem was they didnt erase the misfire code. Computer might not realise and run bad even though you installed new plugs, boots and coils.
erase all codes and take the truck for a drive, if it's still running bad have it scanned again. If the misfire code comes back next step is injectors, the 3 valave is k own for injectors going bad.
WHATEVER you do get this fixed ASAP if you have one or multiple bad injectors you'll ruin the cats on the truck which leads to more money
I'll go to Napa and have them put their machine on it erase the codes on it. I know the guys in there and know their business. It was a Sunday when I originally had it coded and the only place open was O'Reilly's and the kid didn't even mention that and I don't like going there as all the help seem to go to one person for help as they are unknowaldgeable . That's gotta be it, as soon as I put in new spark plugs, the check engine light went off in the dash board but still ran rough so I put in original coil packs and still ran rough. But according to the guy at O'Reilly's that's what the code was, spark plugs and or coil packs. I expected it was the spark plugs, omg were they bad. 171,000 miles on them.
Thank you for the info. I'm handicapped and getting things done takes a while and can't afford mechanic wages at a mechanic shop.