Well, granted our cars like to misfire at idle, but when you change out plugs, you shouldnt have any misses...(My setup was almost identical to yours, and I had a slightly raised Idle, and no misfires at idle)
A clogged fuel filter will absolutely bog the car down, and can create a lean condition, if its clogged badly.
I'd check the plugs first, easiest thing in the world to do...And a fuel filter cant hurt either (though only a year old, it should be just fine)
Best thing would be to grab your tuner, and go for a ride, and log whats going on, to get a more indepth insight of whats going on.