Ok, I've now tried the extra 10k resistor and .1uf cap on the input signal section of the ignition board to make it a one shot trigger per pulse on the hv board. While that works as it was intended, there are multiple pulses coming from the pic chip which really indicates where these are coming from, the pic chip and not the hall sensor.
This is what I said from the beginning. We hooked it up to a scope and sure enough, there were the extra pulses. So, editing the lines for that condition to stop them works. However, it is now pointing to the MSD feature causing the condition!!
Where the lines are deciding how many sparks to produce, and the actual instructions to produce those pulses to the SCR is giving us this condition. So, now we have to actually edit those instructions for a solid operation in the "engine not yet running" condition. Anything over 200 rpms gets us out of that routine and rpm then determines when the pulses will occur. This works fine in our tests so far as we can tell.
Getting there guys! A few more edits and the source code is fixed.

John