Looking at the schematics linked above and the symptoms from the OP, where as one cylinder stopped firing, followed shortly by the second would imply to me the coils are not the problem, it is the CDI module or what ever system this craft has.
Hence the title "home made CDI" and not a request of "Where to buy coils" as this thread has lead to previous.
Or if it is a dual coil firing both plugs together, than it would imply the fault could be after the coil, in the plug leads or the plugs themselves, as why would 1 plug stop if the other is still firing off a dual coil. ??