My feeling is that there may have been another issue close to the main jet ....like maybe it wasnt tight or sealing around the base of the jet allowing extra fuel to bypass the jet , or a blocked air corrector jet. If there is raw fuel ( as opposed to atomised fuel ) flooding the inlet it will tend to go more to the lower cylinder.
My ( M18d ) carb had the main jet corroded in and someone had mullered the screwdriver slot so I bailed and bought a Ali ex carb ( it is identical to the original ) for 30 something bucks .
Awhile ago I did a bit of research ( I read up on others work , not actually do it myself ) into fuel flow thru jets ( weber , mikuni ,delorto ) and basically there is more to fuel flow control than the size of the hole in the jet . There is every chance that a jet with a corroded orifice will flow less fuel due to turbulence .
Pleased you got it sorted