Change the spark plugs and while you are at it, buy new boots and springs for the coil packs and change them as well. I have been around these 5.4 triton engines for a while and have seen and had the same problem. Chances are it is only the plugs but the coil boots and springs are cheap and can produce an issue that most will think its the coil pack. I have had a 99 expy with the 5.4 2v, a 2010 expy with the 5.4 3v and still have my 04 F150 with the 5.4 3v engines and when having the notorious misfire between 40 and 50 miles per hour, a plug/boot/spring change has fixed it every time. I too thought it felt like the rear end or transmission. On your engine, it should only take about 2-3 hours for the work, not sure on the plug number, think it is SP 515 for motorcraft plugs but the parts store will get the right number for you. Also, these engines like the motorcraft plugs best and if they have never been changed, rent the extraction tool just in case you still have the 2 piece plugs that like to break off. Spray a little penetrating fluid in the plug holes and let sit for just a little while before trying to take them out, it will help.
Good luck
Tom