I have a B&S twin that is running very rough. I've replaced both plugs, removed both heads and cleaned 20 years of carbon out. Late last season, I rebuilt the carb and it ran great. I compression tested both cylinders and got 90 PSI from both.

After the compression test, I forgot to hook up the plug wire to one of the plugs and the motor ran perfectly! This is only the case when that particular wire is removed. When I remove the wire from the other cylinder, there is no improvement in performance.

Any ideas! Does this sound like the wire to the coil is bad? Your help is appreciated!

Sounds like the coil is going bad. You can't replace the plug wire without replacing the whole deal.