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

"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.