Sounds like you have a RF interference problem. The HEI is producing some sort of high frequency (RF) that is shuting down your system. We old guys remember the "buzz"th that AM radios had back in the day from same sort of problem. Some possible causes and solutions...
1. Did you change you spark plug wires? Make sure they are of type that suppresses RF. They will act like little antennas to the HEI if not.
2. Spark plugs. They also must be the right type.
3. Wiring to you radio. One cheap and nasy way to cut down on induced RF is to twist your power and signal wires. Idea is...when an induced RF pulse hits one wire with, let's say, signal going one way, it induced a reverse pluse in the other wire, thus canceling the pluse.
4. Shielding. This would mean running as much of your wiring as possible in spiral metallic flex tubing and grounding one end of it.
5. Capacitor. As a capacitor blocks DC and "passes" AC, you can hook a cap. up to your power feed to "drain off" the RF. Close to the radio would be best.
That's a start, other might have better ideas. Good luck.
