1999 Yamaha F100 cuts off while running in cold water

[woodfisher]

Every year in the spring and fall my Yamaha F100 has an intermittent shut-off problem.
It always starts fine and runs for about 30 mins. After it has warmed up, either on start or while running, the fire to the plugs shuts off.
Does not happen during the 3-4 months of summer.
If I wait about 30 mins it will restart. The engine still cranks but no fire.
I also bypassed the security switch to make sure it is not at cause.
It seams to be a short somewhere or some-kind of a safety shutoff (like heat sensor?).
Any ideas are welcomed

[99yam40]

Every year in the spring and fall my Yamaha F100 has an intermittent shut-off problem.
It always starts fine and runs for about 30 mins. After it has warmed up, either on start or while running, the fire to the plugs shuts off.
Does not happen during the 3-4 months of summer.
If I wait about 30 mins it will restart. The engine still cranks but no fire.
I also bypassed the security switch to make sure it is not at cause.
It seams to be a short somewhere or some-kind of a safety shutoff (like heat sensor?).
Any ideas are welcomed

what is this security switch you mention?
and how did you bypass it?

Testing the ignition system when there is no spark should lead you to where the problem is .
but I am not sure what kind of ignition system this motor has.
if a CDI then you should check the charging coils and pulser coils feeding into the CDI , and the outputs of the CDI