anytime i see that problem this is the steps i suggest:
1. ngk plugs? a lot of the honda's i see with this issue have bosch or autolites...blah!
2. stock wires or ngk wires? honda's seem to have issues with any other brand wires. msd sometimes work fine, but if you've already changed plugs try stock or ngk wires.
3. stock cap/rotor? an old or loose rotor will cause all sorts of issues. don't buy the cheap aftermarket ones...get the honda.
4. coil or icm check...swapping a known good dist will usually point this out.
5. check timing belt.
6. if all else fails then check afr, fuel filter, pump, etc.