I would be leaning towards pick up coil as well. Generally a cdi failure starts with intermittent loss of spark to one cylinder, loss of spark to both and then being able to restart after a cool off period is a sign of pick up coil failure.

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.