V6 2002 Mustang hesitates when accelerating

Took it to an independent repair, who put it on a computer. Code said plugs were bad, causing cylinder to misfire. Fixed that and threw in a fuel filter just in case. It was better until that evening, when all the problems came back. Car sounds like it wants to die entirely when dealing with hills, but the problem is there on flat stretches, as well. Seems to deal with acceleration, to the point that it starts to shake, but it just doesn't feel like it's running well regardless--feels like it's an old beater instead of a Mustang. Could something have killed the plugs again, or do you think it is unrelated?

I plan on either taking it back to the independent repair or to the dealership. Car has 78000 miles on it, but I got it new and it hasn't been run badly or anything. Every other '02 Mustang problem (after-market exterior lights, hood paint job, & noisy brakes) has seemed to hit it, so I figure this problem might be something someone else with this car has experienced. If nothing else, a laundry list of what it could be would be very helpful.

Needed a new coil pack. Works fine, now.