A better arrangement is to cross the plug wires such that each cylinder is getting spark from both coils all the time (there is always a wasted spark on these engines anyway). Had I done that, I could have continued with both cylinders working (although not with two plugs per).
For what its worth, I have a setup that seems to cause a lot of controversy amongst the elders but runs like a clock for me. '83 R100, factory electronic ignition, dual plugged, Accel red coils, (single) Dyna Ignition booster. Came to me that way from the PO.