I've never run across this given I don't scope a sensor at high RPM. I'm betting when this second blip gets a high enough voltage and crosses a sensing / noise filter, the ECU thinks the engine is now 2X RPM. This would explain the consistent RPM cut off.

When a CW distributor gets a CCW pickup coil, the sine wave is inverted , timing is altered and sparks occur when the rotor is out of phase. Did you recheck your ignition timing with a light? I'd expect it to have moved from the original build.