I just got a 2005 f-150 5.4L with 97k miles on it a few days ago. Everything was great until I was heading to work this morning and after coming off the highway the engine started to shake once I accelerated. I immediate think that it could be a bad ignition coil leading to a misfire on one of the cylinders. So I get it tested and find out that cylinder 4 is misfiring. I figured the dealership did a full tuneup and changed the plugs because it's almost at 100k miles so I just get a new coil and put it on, but I'm still having the same issue just not quite as bad. Just need some advice on what to do next, or any other ideas on what might be causing the issues. This is meant to be my work truck so I need it in top shape asap.

 

If you don't know for a fact that the plugs were changed, then I would assume they weren't.

 

Why buy a COP before you replace the plug ??.. you could of swapped a COP from another cylinder to see if the DTC followed it.. Try a new plug now in #4

 

Check the filter just to make sure it did not come apart. Probably not your problem but had one give me problems before. Then I would go ahead and change plugs or at the least pull the plug for the cop you replaced and have a look. It may have fouled out.
Tank of fresh good gas with maybe some type of water remover.
Bad plug would be my guess though. Could have went bad due to the bad cop.