[Rick Parker]

Couple of things... are the valves completely closing? If it is a solid lifter cam is there lash when springs are relaxed? If it is a Hydraulic cam, maybe reseting the preload on the lifters??
Next...it is not unheard of for the cylinder that is not firing to have the throttle butterfly closed (not exposing the idle port) when the other cylinder on that carb is functioning properly. This is sometimes caused by a slightly twisted shaft. If the syncronizing tool that you are measuring the airflow shows that both cylinders on the suspect carb ARE drawing an equal volume of air then move to the idle jet and see if something is plugging it, next remove the idle mixture screw on the suspect cylinder and blow small amount of compressed air into it, reset it to correct opening about 3/4 - 7/8 of a turn open.