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Runs on water but not in the water

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I have a 99 GTX limited, 947. Hooked up to a hose, the thing runs great but once I dip it in the water, It doesn't wanna stay running. Let me start off by saying I am an automotive mechanic and I have been trying to figure this out for a couple days now. Cleaned carbs, fuel lines replaced, fuel selector switch cleaned along with a new spin on filter. Fuel tank baffle removed (will need to replace due to bad float in the sender), tanked drained and filled with premium. I did notice the 4 nipples on the baffle where caved in a bit like the hoses were tightened to much. Didn't think anything of it at the time because I thought the fuel flow wouldn't be restricted all that much. Compression is good, 135 in each. Obviously it has good spark. I have a shop manual so I have been going thought the procedure of setting low speeds, fuel accelerator Gap, idle speed, throttle cable, oil pump cable.... I'm at a loss, any help would be greatly appreciated.
 
Did you rebuild the carbs with all new Genuine Mikuni parts including needles and seats?

Cleaning the fuel selectors doesn't work, they have to be replaced. Easy check is a temporary hose directly from the tank to the carb.

Is the idle set correctly at 2,800 rpm out of the water & 1,400 in the water?
 
Did you rebuild the carbs with all new Genuine Mikuni parts including needles and seats?

Cleaning the fuel selectors doesn't work, they have to be replaced. Easy check is a temporary hose directly from the tank to the carb.

Is the idle set correctly at 2,800 rpm out of the water & 1,400 in the water?
Yes genuine Mikuni rebuilds

I have tried from the tank to the carbs (no change) but only at my house hooked up to a hose where it runs spectacular, I could do that at the lake although is it really possible that restriction/cavitation at the switch would cause it to bog down and not be able to idle in the water but the complete opposite out of the water?

I had the idle set at 3000 out of water, in the water I have to give it throttle to keep it running so I don't really know.

Should the spin on filter have air in it or should it visibly filled all the way up with gas?
 
Square oring? I have a round one, and it has been changed. Also did a pressure test, I made sure nothing was hissing or dripping from the lines but I didn't moniter the pressure over 30 minutes like the manual says. That being said, it doesn't appear to be leaking from the water separator oring. Also the check valves appear to be doing what they are suppose to do in the pressure test.
 
Just purged all the air out of the water separator. Pretty sure it was from doing the fuel lines I just wasent sure if it needed to be free of air. It's been sitting for a bit now and it looks like it's still free of air. Is that a pretty good indication of an oring that's not letting air in? Or could it still be letting air in causing it not to run under load?

Thanks for letting me pick your brain, I just can't help but think I'm missing something simple.
 
Those seal are known to be problems they allow air in when running when they fail. To cheap to worry about not replacing order multiple
 
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