If your carbs worked fine in the other ski, in my opinion your problem likely lies elsewhere. I cannot see how carbs can just come back to life like that.
I would try replacing all your fuel lines, and pulse line. First I would try running without the inline fuel filter. Did you look at your...
I guess you just have to price it assuming you might have to replace the motor and maybe some other stuff. Motor could be dead, have water, ... you’ll just will not know. I guess if you have the time you could pull the head and see if there is excessive corrosion/rust.
Definitely see if you can...
Did you try removing the in-line fuel filter and see if the problem changes? I know you said you cleaned the fuel filter, but I have had a new fuel filter be a problem before.
Also a carb rebuild or at least a take apart and clean (especially checking the small basket fuel filter).
Good luck
If you have not done so already, tweak the high end adjusters up (and down). You are likely getting too much fuel or too much air, and this will compensate. I would tweak them a quarter turn at a time.
Not sure if you are testing dry or in the water under load. Final test would need to be in...
You can get the orings from McMaster-Carr... apx $3 for 2, maybe $11 with shipping.
See this old but good thread...
http://www.x-h2o.com/index.php?threads/yamaha-is-this-a-pro-tec-rec-head-o-ring-problem.40381/#post-546199
If it is not cranking at all, could try new plugs, could try new plug wires/boots (especially since you get no resistance between them), could try a different battery or jump from a car battery.
Are you getting any spark?
CDI is a possibility but might want to try these less expensive options...
I have 3 superjets and there is always some water in the hull after riding. An inch or two of water is not abnormal (for me). I do have bilge pumps in each... in my opinion, a bilge pump is really a necessity
Sounds like it might be overheating. Do you have a pisser? And is water flowing out at a good rate?
Might want to check your coolant line(s) connections, and assure water is flowing throughout.
Less likely, it could be a slow exhaust leak, starving the carb of air. But that would typically clear...
I forgot that the first batch they sent did not match well. It was from their east coast facility. I complained and got it replaced from their west coast (CA) main facility. This batch matched.
Zip ties. I have an aftermarket pole so my situation is not the same, but my chin pad has been attached with zip ties for a couple years now with no problem. I know it sounds hokey/cheap/whatever... but seems to work.
This may sound like an ignorant suggestion, but it solved a similar problem I had a few years back.. after much effort swapping parts. It ended up being a bad fuel filter. For some reason it passed fuel without a load, but once in the water it would only barely run in the low end and would stall...
The 3500-4700 ohm range is for a 701. Guess I cannot be certain it is the same for a 650. Although I would guess that they are. It is essentially the resistance across the coil and I would think the coils are the same. Happy to be corrected.
Also, in my opinion, the weirder and more...
Could check the resistance between the spark plug boots. I think it is supposed to be between 3500 and 4700 ohms. If not, could have an issue with the sparks plug boots, wires, or the coil. Not sure if the coil is swappable from a 701, but the boots and wires are.
For the compression test. Should be around 150 psi with less than a 5 psi difference between each cylinder.
Most important is to take it for a test ride. A ski can sound great on shore, and run like crap under load in the water.
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