MS3 Pro and MSD 6A and mis fires above 3000 RPM

Bewy said

"Reducing the coil 'on' time the coil had more time to charge"
Maybe I am misunderstanding the statement but it doesn't make sense to me.
I have no experience with M/squirt but if your dist is using a magnetic pick up, they can be very susceptible to inference from HT leads, coil [-] wire & coil itself. Wires too close will induce enough voltage into the p/up wires to cause false triggering. I use coaxial microphone cable for p/up wires, with the shield grounded at one end.

Click to expand...

Duty Cycle is how long a item is switched on. Reducing the Duty Cycle means the item is not on as long. In the case of an ignition coil reducing the Duty Cycle allows more time for charging the coil. I am sure you know how ignition coils work and that the formation of the magnetic charge that collapses when the coil is switched off to make the spark that fires the plug does not happen instantly. Reducing the Duty Cycle allows more time for the magnetic field to develop and allows the magnetic field to be stronger, to a point. Reduce Duty Cycle too much and charge a coil too long and one just generates more heat.
Working with FI and magnetic distributor pick ups I know about EMI interference. Later I will link a post I had made here at FABO a couple of years ago after I worked through an EMI issue perhaps like yours, resolved with metal shielding and improved wire routing.