When my cdi went bad at 40,00 miles one cylinder would intermittingly stop firing, then kick back in then cut out again. There did not seem to be any pattern to it. Replaced it and never had an issue again. A bad coil would follow would over to the other cylinder when you swapped it over. A bad ignition pick up sensor generally manifests by the bike cutting out all together after it gets up to operating temperature then starting back up after it cools down, then cutting out again once it has warmed back up.
2006 865 Neon Blue/Jet Black Speedmaster,790cams, TTP Stage 2 Firestarter, Epco Exhaust with 10.25" Samson Vrod baffles, UNI pods with 40 pilots, 150 mains,Thruxton needles, 3 turns out.
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