I'mnot familiar with the two coil installation, don't know what kind of clearance you have with the electrical connections on the coils .
When I installed my firsr DYNA coil on my '81 R65, I put the wire connectors on the primary circuit of the coil pointed away from the backbone frame tube, when I installed the fuel tank, the engine wouldn't start, adjusted the connectors and the engine ran fine .
Like I said, just a guess on previous experience .
Have you done any work on the ignition system lately ??
If you have,you may want to go back and look over the area(s) you worked in, maybe something is loose, etc ........