04 yamaha waverunner,1100 HO, starter doesn't engage but once every 20 times the start button is hit,it clicks but doesn't roll the engine over,but about every 20th time then it just rolls over 3 or 4 revolutions before disengaging. Battery is brand new and will start my chevy pickup.changed oil,fogged cylinders last fall,pulled out spark plugs so its not compression.

SOURCE: CLICK CLICK CLICK

I would take the battery up to advance or autozone and get it tested under load. The battery may show 12v but not have the amps to crank

SOURCE: I have a 1994 Yamaha 40 HP 3 cylinder 2 stroke

all 3 carbs had A  clogged jet totally dis assembled and cleaned the carbs put them back on and the engine runs great I will need to fine tone the needle valves once I put some fresh gas in it. 
Thanks John

SOURCE: starter cranks to compression stroke and stalls

check your valve. your riding on high compression could damage other components don't try to jump start ether. if your valves are ok it my be your MCR on your cam. if you have a ohv B&S Avr this is comen, valve should be set at .05. you real should have a profeshionl do it

SOURCE: i have a 1998 yamaha waverunner XL1200. when i hit

It may be your starter relay if it is clicking from the CPU box

SOURCE: 2004 fx CRUISER ho WAVERUNNER DOESNT WANT TO IDLE OR RUN AT TOP S

did you mean 900 cause 9000 is overrived and the engine may be blown