I would have thought problems deeper in the fuelling system/ECU/exhaust would have thrown a warning light & would therefore leave their code on the ECU. Might be worth getting a scan. Can you detect whether you are losing both cylinders, or just one - not easy I know. My neigbour sorted out an issue with his bike, by carrying a lazer thermometer with him. When the bike started playing up, he pulled up promptly, killed the engine & took temperature reading off both headers. It identified the cylinder playing up, & the problem was found to be a tight exhaust valve.
However, my money is on the coil sticks breaking down too. Maybe water ingress down the plug socket. Commonplace in my K16 days - starts off barely noticeable, just the odd stumble, then gets worse progressively. Doesn't always throw up a code in the early stages. Not so bad when you've got 6 cylinders to play with though.
However searching the parts bin of random thoughts: -
Side Stand switch - suffered it with a Kawasaki twin. At certain revs, when engine vibes peaked briefly, the side stand cut out would intervene all on it's own. Disconnected the system, including the clutch interlock as a quick fix & ordered up a new switch once proven, as the original was corroded beyond repair. Also checked out & replaced the local wiring/connectors.
Fuel cap/tank breather - again on another Kwack. the fuel tank breather was blocked & the bike would cut out randomly after about 10 miles. Seems a bit unlikely with our pumped system.
Injectors - usually pretty reliable these days, but endure harsh conditions. Crap fuel/water & diesel contamination could impact. Seafoam? My old Hayabusa picked up copper contamination from the fuel pump, which caused injector problems - didn't throw a code initially, when just the odd stumble, but did cause a panic when it worsened during a tour around Spain/Portugal.
Plugs & electrical connectors - a mate of mine didn't seat down the coil stick firmy, so it was bouncing around on the plug top, causing a misfire induced by engine vibes. Turned out he had damaged the coil stick, when removing it for a plug change. Expensive mistake.
Alarm - I have known these play all sorts of tricks, particularly retrofit. Usually crap wiring, or cables pinched. Zapper can play up too, usually from being left attached to the bike keys & shaken around in all weathers when riding. Keep the fob separately in your pocket.
Hope you can track it down - keep us posted.................... KEN