I had a similar problem with my 2000 RK. I had a rock fly up and hit the voltage regulator. The engine light came on a little while later and went out a second or two later. This went on a few more times. About two weeks later while riding, the bike started acting like it not getting any fuel and it would die. Sometimes it would start right back up and run fine. Other times it wouldn't. Took it to the shop several times and it would always run fine for them. No codes either. Finally the mech hooked a computer to the bike and strapped it to his leg and rode the bike till it failed. Found out the regulator was intermittantly going over voltage up to 18 volts. This caused the overvoltage protection for the fuel injector system to shut them down, thus causing the bike to stall. Replaced the voltage regulator no more problems.