2004 waverunner fx cruiser, ran great last time out. Now hard to start and wont run on high speed. Nothing over 6 mph.

remove the carbs and have them professionally overhauled
indicates a problem in the high speed circuit , probably a blockage
might also be an incorrect float level that is not allowing enough fuel into the bowl for hgfh speed operation

Robert, First try new plugs, check fuel filter, sounds like it could be carburetor/injector issue, dirt,plugged jet, etc. Remove and clean/rebuild carb./injector.
Check the attached links,instruction and guides, Good luck
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XLT1200 Bogs down
Thread 2004 FX HO ECU Problem
Waverunner Loses Power and Wont go Above 35 mph Solution
https://answers.yahoo.com/question/index?qid=20080525091900AATkgJh

you may have to check the pump unit for obstruction
the impellers are known to wear from abrasion from sand in the water and not operate efficiently.

check impellor blades not bent ! scoop grate not bent ? wear ring not badly worn ?not got some rope or debrise on impellor ?

Pull your air filter out and also replace plugs. Overtime the filter will become saturated with oil and believe it or not the plugs can cause about a 10 mph drop if there going bad. But make sure your pump and impeller are not damaged also

what is the answer to this question?

is it running on all 4 cyls ? did you drain the water out of exhaust system then fog the engine properly before storage ? if not then valves stick open due to damp air coming back from exhaust ! head strip etc !!

remove all sparkplugs and hold full throttle and crank over several times to get water out of cylinders ! have a jump pack ready as battery will die ! use carb cleaner on the plugs each time you try to run after this , hope this has only just happened as internal damage might already started ! if all ok check the engine oil also as water normally gets in after this problem ! if oil is milky then change oil several times , run for 15min on hose each change until oil normal colour ! then you must take for a run for an hour to help dry it out !

Nevermind those other answers, if its running on all 4the cylinders but just real sluggish and missing top speed then listen up, let's first rule out the possibility of a damaged impeller, now locate your airfilter box and remove the filter, just throw it away because last I checked dirt really doesn't settle on top of water, now locate your throttle body and remove the intake tube from it, now take out the 4 bolts that hold it on and find your flame arrestor element. I've dealt with this problem many times only to find out that the geniuses at Yamaha had installed this screen right after the butterfly which accumulates airfilter material and clogs

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