It all comes down to Timing

I started doing a lot of digging on ducatipaso.org and the original Ducati Maintenance Manual. The more I read the more I realized that the flywheel was the problem. With two ignition pick-ups I needed a single flywheel pick-up point instead of a flywheel with 4 pick-up points.

I found a newer Kokusan flywheel on ebay, purchased it and waited for it to arrive.

I installed the flywheel, reset the two ignition pick-ups. Set the timing with a timing light. Crossed my fingers and attempted to start the bike.

The bike started and I warmed it up and took it for a ride.

Success, no engine miss-fire at 5000 RPM.