The issue may be with the ignition module not allowing proper charge time or its "gate" bleeding through with the increased resistance required to create the higher secondary voltages. It could possibly be your plug wires if they are not new or decent quality. The voltages could be leaking to ground and causing the issues.
I have an Accel Super Coil in the HEI on my 84 Camaro and it has never causes issues. I am planning on trying an Accel on my Sierra as well when I do the tune-up. I run NGK plugs and Accel's 8mm custom fit plug wires on it as well.