This quote from your original post is very similar to my experience with a faulty throttle position sensor. I had noticed what appeared to be a trans vibration or engine misfire occassionally that was getting more frequent, then at 60 mph my car did what you quoted and I limped home with a message center warning. The problem disappeared on a restart. My Ford dealer could not definitively pinpoint the problem but suspected the throttle position sensor. It was replaced and the problem has not occured again in over 2 years.
Your vehicle has an electronic throttle control (throttle by wire) similar to mine. A faulty sensor will cause the PCM to position the throttle plate incorrectly and give rise to all sorts of driveability issues.
Once the sensor is removed, it must be replaced with a new one or poor engine performance will result. Based upon other people's issues with the electronic throttle it appears that the sensor may include a return spring for the throttle plate that can fail or partially fail. There are electrical connectors for the sensor and the throttle motor that may be problematic.
Just an alternative to the plugs and cops and fuel delivery and vacuum leak issues that may fit with the intermittant nature of your problem.
Good luck.
2002 explorer 4.6, same herky jerky while accelerating and/or cruising between 40=60mph. I bought a scan tool to avoid lets try this method. After the fact, I wish I had done more homework on this before purchasing, I would have bought one that also gives you live data, that will help you to truly diagnose your problems. You will get your money back on this for sure. Hooked up the scanner and retrieved these codes, P0305, P0308, misfire codes. This truck has 205,000 miles on it so I started with the basics, fuel filter, plugs, air filter and cleaned the MAF sensor, (using approved cleaner). After doing this, the truck ran better, but still had that nasty herky jerky while driving. I then replaced the fuel injection pressure damper located on the fuel rail passenger side, and cleaned the throttle body. This too did help a little, (obviously the fuel system had never been maintained over the first twelve years of life, so it did help). So, after more reading on this forum, a lot of people point to the MAF being bad, but I did find a few posts talking about the throttle positioning sensor. I did replace the TPS, (now I'm using the let's try this method), and I must say, it made a huge difference. Now while driving it is smooth, no severe herky jerky. I did notice a slight miss in the engine while under load and finally, the light comes on. P0306. I replaced the coil on this cylinder, it's like a new truck, all of the pestering issues are gone,,,,,,,,,,,, for now. Yes, I did replace a lot on this truck, almost all was overdue maintenance that had never been done, even the plugs were original. With all of the crap being put in our fuel these days, I recommend maintaing your fuel system regularly. The scan tool did help by pointing me in the right direction, when given a code, but this forum does help as well. I never read this much while in school... So thanks to all who are offering information here.