I had a miss on #4, and a fouled plug which came back within a couple weeks of changing plugs. Eventually I found some residue (gray dusty-looking crud) on the #4 wire where it exited the coil. Replaced that coil and things got much better.
That wasn't all there was, as I still have a very occasional miss, and my mileage is not what it should be, but that new coil helped tremendously.
The most common point of ignition trouble on these bikes, though, is the wire into the plug cap. The cap just screws onto the plug wire, has a little pin that pierces long-ways into the end of the conductor. Kind of like a wire nut, but inside out. Corrosion there will kill your spark.
To remove the cap from the wire, just hold the wire near the cap and turn the cap like you were taking a nut off of a bolt. If you find corrosion in the end of the wire, just cut it back a quarter inch or half inch, clean the pin in the cap, and fasten it back on.