Do a full tune-up first, including a distributor cap and rotor.

It could also be a clogged or defective #3 fuel injector.

Is the alternator belt a Honda OEM belt? Poor quality control on aftermarket alternator belts have been known to set off misfire DTC's in 6G Civics, 96-97 del Sols, and 1G CRV's. Strange, but true.