Just spent the better part of the morning diagnosing a problem with my 12 year old, 2000HR, genny. It would start ok, but not run unless the bypass or prime button was depressed on the power panel. I disconnected the "brain box" as the PO had trouble in that area and after re-connecting same, problem resolved itself apparently. My question now is WTF?, and does anyone know how to replace the 20 and 25 amp fuses that appear on the face of the panel? I initially thought that would be the source of the issue. The manual from Kilopak is a joke BTW.
Some crude thoughts; Holding down the bypass switch will keep the genny running if it thinks it has a fault. Depending how fancy the fault circuit is, the genny may or may not make electricity. Disconnecting and reconnecting the brain box and then the problem went away? Suspect bad connection or wire somewhere. If I remember, Small KiloPaks used Kubota engines, Stamford gen-ends and there own relay fault/run box. The relays should be easy to replace. Let us know how it turns out.
Chances are it's a bad shutdown sensor, either overheat, oil pressure, etc.....disconnect them 1 by 1 and run it and that will tell you which one it is.