Ok. first off. I would start with the basics..
Clean MAF, and the TB. replace the pcv valve and run a can off sea foam. If this does not help
Then i would go for plugs and coil packs.. I would recommend replacing the coil packs with the plugs, if you can. Since you have to take them off to replace the plugs anyway. Look around. I would not really the prices for the stealership. I would look into local parts. look at all the options. For me locally hear in utah. I was able to get all the coil packs in accell for way cheaper the oem replacement.
For me. Dealer was 98 bucks each. Orileys for oem was 38 bucks. I got accell performance coil packs for 24 each.
The other tip is to use MOTOCRAFT PLUGS ONLY. Their are a few that has good luck with other plugs. For some reason aftermarket plugs dont seem to work.