my 2004 Yamaha 250CC 2 stroke has an alarm going off and I cant figure out for the life of me why.Checked everything from oil to gas and still cant get it off. Any help would be great.

overheating, and low oil in the main tank {on the motor} I believe are the only things that will trigger an alarm
Doesn't the gauge tell you why it's happening?

On the Merc Opti's almost anything will trigger it, bad injector, etc... it goes into a low-power mode so you can't fry the engine..

but the occum's razor solution is oil or water....

is it still running?

not that the alarm went off right before the bolts on the compressor pulley sheared....

I hate to break this news to you but those Yamaha 250 2 strokes are the biggest piece of %$%$%$%$ Yamaha ever put out !!!
1000s of them blown power head around 400 hrs !
Go to the Hull Truth and do some research and you will see

boat starts up and runs no problem water comes out of the water jet right awaywhen started it so its not a over heating issue as I first suspected. The one catch is I had to drain water out of my fuel tank when I unwinterized it.

Do Yamaha'a have a service engine soon warning? My Suzuki does at every 100hrs.

just because it's peeing doesn't mean it's not overheating, could be anything in the cooling system, the poppet valves on those are notorious for salting up and sticking, also might want to check the thermos, is this in the water or on the hose, alot of those bigger Yamaha's don't like to run on the muffs, I have a friend with the same problem, overheats in the yard but not in the water