Could be 1 of several things but where I would start....
Since it does not happen during mixture enrichment times (warm up w/ extended injector duration or "choke" times), it almost points to a lean fuel issue or a lean miss. As soon as the warm-up enrichment period ends, the bike experiences the miss.
Something like lower than normal fuel pump pressure, a small air intake leak, 1 injector having a poor fuel spray pattern, fuel filter having poor flow, a pin hole leak in the Hi pressure fuel pump line inside tank, etc. Something that creates a leaner than normal mixture. Anyone of these issues usually gets worse with time, just like your problem has.
For now I would rule out electrical or ignition since it does not happen under hard acceleration. That's the time when the ignition system is under highest demand.