ok.. i've flogged a honda superhawk for 32,000 miles and tore it down.. heres what i found after hearing the EXACT same knock your describinig and my theory on it..
valves, buckets, lifters, everything all within spec.. i mean EVErY VALVE.. the odds that your RC will have valves out of spec AT ALL....EVER.... are slim to none.. most honda engines i've ever spec'd (inline fours especially) are very very well built and hardly ever need valve adjusting
both cylinders within .05mm out of round/taper no scoring
both pistons looked well, no bad scorching or skirt damage, but were slightly out of spec (skirt to skirt) the likelyhood you're hearing piston slap is nil
connecting rod plain bearings had some scuffing on them, presumably the knock i heard near the crank, lower in the motor and only when low revving the motor away from a stop light... i can only theorize that during low rpm operation, these huge pistons overwhelm the oil surface under low rpm pressure and cause a hydraulic knock or an actual metal to metal contact on the con rod big end... my advice for you, stop lugging the motor, give her some revs like she wants and ride the rc like you mean it..

:twocents