There's a 95% chance it's a COP going bad, causing a intermittent low grade misfire. Which will be hard to track to a particular cylinder. The best thing you can do in that situation is to mimic whatever it takes to cause it to buck and keep it bucking for as long as you can and hope that it trips the CEL. Most of the time you can find that sweet spot right around 40-45mph when it shifts into overdrive with light throttle applied. What I'm saying is, force it to misfire as much as you can... hopefully you will either get the CEL to flash, or come on. Then the DTC can be pulled to determine which cylinder it is.
And, since it sat for 2 weeks, if your using ethanol blend gas, there's a chance it could have separated. Techron fuel treatment is the thing to use.
If you changed the fuel filter at 35k, it should be fine for a few more miles. 15k is a good mark to change them at.