You sure you have fuel and spark when it doesn't start? I' assuming it cranks fine but no fire? It sounds like a classic honda main relay going out. That's exactly what they do, will start fine then bam, no start just crank.

I would start it up about 40-50 times, then let it rest and charge the battery for a half hour or so, then do it again until it fails to start. Have someone continue to crank the engine after it refuses to start and go loosen either the inlet banjo fuel fitting at the fuel filter or the inlet at the fuel rail and see if it shoots fuel out. If the relay is good it should soak you with fuel while cranking. if it's bad you'll have no fuel coming in from the fuel pump.