If it's fine at higher rpms, I doubt it's the fuel filter, but not a bad idea to change that anyway. Normally I'd assume it must just be something electrical, like a coil on it's way out, etc. but since you mention it's a VTEC-E - those do switch over at around 21/2 to 31/2 thousand rpm if I remember correctly.

Tune-up(plugs,cap,rotor) and filter aren't a bad idea, but I'd hold off on new wires unless you see cracks in the insulation or their resistance is out of spec.
Also, noticing an increase in acceleration as you let off the gas, like if you're at WOT and slowly give it less gas, and notice the car picks up in acceleration just a bit, is often a sign of the ignition timing being off. You could be running at max. retard (dist. cocked towards firewall), although that by itself shouldn't make it feel like the engine is missing.

Perhaps the timing is too advanced, I've never driven a car that was at full advance, close but not quite. Maybe it's enough to cause detonation at those rpms (despite the best wishes of the knock sensor) :shrug: