have you tried a different coil
Yes, try switching the coil and see if the 'miss' migrates to the new coil location.
Actually, your description is a bit puzzling. You say that at higher speeds, the bike seems to run fine on all-four. I am not familiar with this type of coil failure, usually either a coil works, or it doesn't. In my experience, a plugged pilot jet will cause a cyl to not fire at idle, and by 'not fire' I mean that there is an uneven cadence, where that cyl is obviously
not-firing because the idle circuit is not providing gas, and not-that the coil is defective in function. When you increase revs, and the carb needle and the main jet are metering the gas, the plugged pilot jet no-longer is interfering with the delivery of gas, the cylinder begins to-fire, and the bike will pull normally.
On the early 1985-'89 ignition, if the TCI ignition box begins to have problems, then you may lose one or more cylinders, you have the 1990+ box, and failures of those are more-rare. I've heard that trying to re-solder the fine-wire terminals from the plug disconnect to the circuit board inside the TCI box may help restore an intermittent or an absent spark. The people who have had success with this usually attribute the repair to a cold-soldered joint which fails, needing re-soldering. A cold joint may appear dull in-color. Also, those wires to the terminal board are fine-gauge, and could fracture, usually from vibration.
One of the other things to do is to remove the weak cylinder's spark plug cap, and to check the high-tension wire conductor for any green corrosion, if you spot the green corrosion, trim about 1/4" off the high tension wire end, make sure that the spark plug cap screw inside the barrel of the spark plug cap, to-which the high tension wire attaches is clean, and re-connect it. That has proven to work to solve a problem like-what you've described, where corrosion between the spark plug cap and the high tension wire interferes with a good connection, causing the plug to mis-fire or to not fire, at-all.
