Interesting perspective. I just got all the stuff on I bought from you (J.G. in Nor Cal) and jetted it to your specs and it runs fine, no miss with just the Dynatek non-programmable.
These things really fire at 15 degrees ATDC? That seems to be a major step backwards, my experience is with V-8's, but I always liked 32~36 BTDC on a no nitrous no blower engine.
This problem, in my mind, is electrical. With you finding 7 degrees difference from advertised timing curves, something isn't right. Is Dynatek Q.C. up to par?
I can see people jetting themselves into a miss, but adding a box and getting the problem sems pretty clear. If changing the coils covers it, then something is going on with the coils and their interaction with the box. If the carbs are up completely on the main jets at that point, then it stands to reason the miss would get worse, not clear up, as more fuel is needed and not forthcoming. It would just lean out til it dies.
Timing could be impacted by how fast the coils saturate and discharge when signaled to do so. It does not take delay in that process to move the curve a couple of degrees. Every performance dist. I ever ran, (again, V-8) had all the timing in by 2000 RPM, or sooner. Timing not keeping up with an engine gaining RPM means, in essence, that the spark is happening later, and a miss. Firing the plug when the piston is already heading south 15 degrees on the power stroke seems like the ragged edge.
If the engines that are missing could be read on a dyno with good numbers printing I think this would be found quickly.
Helluva mystery, tho.