That engine will have hydraulic valve lifters. It's possible your builder has the valve adjustment a little too tight, and the lifters are keeping the valves slightly off their seats as the engine warms up. Try backing all the rocker arm nuts off 1/4 turn, and run the engine again. There's also a remote possibility of some voltage feedback from the alternator to the ignition system keeping the coil energized for a short time after the switch is turned off. Try disconnecting the big charging wire at the back of the alternator and running just on the battery to see if the problem goes away.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
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