I went thru a similar thing earlier this year, the right side spark would be lost after the bike had been stopped for 10-15 minutes and then be okay after a while longer. (thought that the ingnitor was going bad) In the effort to isolate the ignitor I tried swapping the coils right for left. In doing that I tightened all of the coil mounting screws and adjusted the fit of the HT wire to the coils. Diclectric grease on everything as well.
So far a couple thousand miles and no lost spark.

05 speedmaster - 1100cc, 11:1 racing pistons, Carillo rods, thunderbike cams, ported and polished head, 2mm over intake and exhaust valves, Barnett kevlar clutch, scepter pipes, oversize manifolds, 45mm HSR's, TTP stage 4 firestarter