Two years with a non functional breather drain and water blocked sponge could have collapsed the filter mesh paper making if it choke off the air supply. Paper distorts with water vapor and clogs with oil vapor from the engine. Honda recommends renewing the filter every 6 months and assumes the engine vapor recovery system is clean and functional. Wouldn’t you be a little embarrassed if a new filter fixed your sooting woes?
However, there is no good reason for any cylinder to show different plug deposits than the others. If the soot is coating the center electrode insulator, that provides a path for spark energy to avoid jumping the gap.
Check for carb coupler leaks, manifold oring leaks, Fuel level equal in each float bowl (clear tube check). Emulsion tube hole blockage in the carbs, jets and needles same size in each with no wear marks. Pilot screw position?