Sounds like a plug to me. Take them all out, and inspect them.
I had the same symptoms, and I thought I had some serious internal damage. I took out all the plugs once, and they all looked fine. Did a few more things, then inspected the plugs again. The ceramic had cracked on one of the plugs around the electrode.
It's not the fuel filter. And whoever paid $100 is crazy. You can buy one from the dealer for $30 or less, and change it yourself in 10 mins.

Does it smooth out when RPM's increase?

I'd be willing to bet it's a plug. Post the results.