The misfire is solved. It was a combination of buying a motorcycle that was already partially taken apart and my inexperience with the engine, but I worked through the problem. Now she is running very smoothly. Before and After audio links.
So what did I do wrong? I connected the leads from the coils to the spark plugs incorrectly. The left coil had leads labelled 1-3 and 2-4. The right coil had the same labels, so I hooked them up to the spark plugs from left to right in similar fashion. Cylinders 1 and 2 from the left coil and cylinders 3 and 4 from the right coil.
The correct connections are the left coil to cylinders 1 and 4 and the right coil to cylinders 2 and 3. Why would they make them cross-over?
This image shows the the incorrect and connect lead connections:
All of the adjustments I made trying to improve how the bike was running on two cylinders instead of four were for naught. When I started the bike on four cylinders the RPM’s were double what they were before at idle and rising. A quick adjustment there and it was running smoothly.
I then hooked up the vacuum sync gauge to the carburetors and found that I had completely screwed up my bench sync trying to synchronize the carburetors when only two cylinders were functioning. You’ll see what I mean in the next update.