Though, the coils *could* fail in other ways (that wouldn't introduce a problem on the secondary, but which could cause an intermittent open on the primary). Not the usual failure mechanism for the dual coils, but I don't have direct experience with the single coils to say one way or the other. I would try swapping the plug leads to the coils and see if you can get the problem to move from one cylinder to the other. IF so, it is most likely a bad coil. [Edit: Or plug/wire]
Is this bike still running with the points ignition? IF your condensor (capacitor) is dying it might possibly cause this sort of thing too with a weak spark.
Perhaps Barry's amplifier kit find might also be of interest to you, after this is all sorted out - the amplifier should (if you disconnect the condensor as described) give you longer points-life, too.