Even if the bike runs like that, something is wrong. I surely wouldn't run the engine even a short distance with that symptom. It takes some elaborate modification to get the magneto to deliver maximum current and exact timing with a modified breaker cam. Even if the breaker cam could be modified to that extent that the ignition timing is right with the front wire to the front cylinder, the magneto rotor needs to be timed so the magnetic field is shifting direction at the exact moment for best transformation strength. That is called azimut. With a V-twin, that azimut needs to be compromised a little since the best strength is 180 degrees apart. The magneto factories made a lot of research to get that just right. I suspect strongly that something is fiddled with in your magneto and not sure if it will be allright for a Scout V-twin engine. The timing and strength of the spark can be checked with a oscilloscope on a test bench.

Still, you need to get into the theoretical and mechanical workings of a magneto and check that everyting is allright, a small fault can really fry the engine and that is expensive and unneccesary.

A scientific restauration with the right knowledge and tools, with proper description and illustrated is done here by Magnetoman. It is about a rotating coil armature, not the rotating magnet as it is in the Splitdorf S-NS and RM magneto, but it shows the level of research, knowledge and presicion is needed to truly know what and how to get all things right in a magneto.

 http://www.britbike.com/forums/ubbthreads.php/topics/508762/1