Have you checked the kill switch for possible dirty contacts? The switch contacts can get dirty over time just sitting in the run position and can cause the now it works and now it doesn't work. The switch is not sealed so dirt and grime can get on the contacts. Clean using contact cleaner. If you take the switch apart remember their are small parts inside that are spring loaded to the fly apart position! I believe the the side stand switch and the kill switch are in series. I faced a slimmer problem (95 K1100RS) and a dirty kill switch was part of the problem.
With the key on watch the fuel gauge as you flip the kill switch on and off, the gauge will drop to zero when the kill switch is off and come back to life with the switch in run, if the gauge doesn't come alive with the key on and the kill switch on, theirs you problem (or at least one of them).