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So it doesn't appear to be the spark plugs...need some help here - RESOLVED

you should have a hatch on your rear cockpit deck to access you fuel sender and pumps, at this point it would be worth and probably pretty easy to pull them as Glassman suggested if nothing else but to look in the tank for debris, but I would pull them out and put them in a can to confirm they are pumping, it's not a simple job but should be easily doable,

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In my 30+ years of diagnostics work I've always found it better to start with the easy stuff first. I think bypassing the switches would be fairly simple to try. Dual pumps, dual pick ups and I believe dual filter socks. Just seems odd that both would be clogged to the point of not starting. Is there only 1 filter? If that's the case I would then start there. I would start with common items that affect both engines. Fuel, engine cutoff lanyard, electrical. Just my .02. I could be completely wrong on everything.
 
In my 30+ years of diagnostics work I've always found it better to start with the easy stuff first. I think bypassing the switches would be fairly simple to try. Dual pumps, dual pick ups and I believe dual filter socks. Just seems odd that both would be clogged to the point of not starting. Is there only 1 filter? If that's the case I would then start there. I would start with common items that affect both engines. Fuel, engine cutoff lanyard, electrical. Just my .02. I could be completely wrong on everything.

If you recall, it was one engine first, then the other, then both. If there is a bunch of crap at the bottom of the tank it would be reasonable for it to happen like that. First one filter clogs, then the other. The common item here is the tank and the fuel in it.

The easiest way to determine if A-the pump is pumping and B-how much it is pumping, is to disconnect the fuel line at the front of the engine, place it in a catch can and turn the key - you don't need to crank the engine. If it's pumping you'll soon see. If it isn't, then I would pull the pump and check the filter. If it is pumping, you have a different problem.

That's the procedure I used to test my Racor fuel/water separators prior to buttoning up the install. I wanted to make sure fuel was flowing through the filters properly before finding out the hard way...on the water.
 
I'm not convinced what the issue is yet. That's the fun of it!

With that rough running I bet you will find a nice surprise in the bottom of your tank.

Had to edit my comments here as I get threads mixed up...
 
Im going to take a stab at this, if the pic of the spark plugs are correct t. They are dark. The plugs should be a light tan. Your plugs show they are Fowler and the motor is running rich. To much fuel to burn off causing g it to run rough.
 
Like some have said not enough air flow or injectors blown out, doubt that since you said all the plugs look the same way, black. Im leaning towards on electrical problem. Could be the coil packs not generating the right spark, letting fuel build up and causing the rich burn in the cylinder
 
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I'm not convinced what the issue is yet. That's the fun of it!

With that rough running I bet you will find a nice surprise in the bottom of your tank.

Had to edit my comments here as I get threads mixed up...

I hope it is a nifty tattoo like I just found in my cracker jack box!
 
Fuel filter was clear, bottom of the tank is clean. I checked the operation of the lanyard switch with the YDS and it showed the status properly on/off when engaged or disengaged. I taped a couple of nickels to the cleanout tray hatch to make sure I am fully depressing the switches in there. I am giving up at this point. A guy I know here rents out PWCs and a couple of Yamaha boats and he has a mechanic that he uses to work on his stuff. He will take a look at it first thing next week. Bummed!
 
probably a wise choice since the easy/obvious ones have been checked, at some point our amateur trouble shooting has to be replaced by (hopefully) a competent professional for a faster and probably cheaper diagnoses and repair. good luck and keep us updated,
 
Have you checked all fuses in the ECU box?

And checked if fuel was flowing like glassman described above?
 
I did check the fuses - there a 3 amp and a 20 amp and they all looked good. I just went with a sight test as when they blow it is usually noticeable. Just in case though I switched the spares with the ones in use. I never did actually pump fuel, but, when I removed the fuel pump from the hose supplying fuel to the engine the hose was full of fuel. And just to make sure I splashed some in my eye. Good thing I was not burning the @Glassman aromatic candle at that time!

I'm wondering if it could be the batteries. I noticed on the YDS that when I turned the key the voltage dropped precipitously. I opened up the batteries to look at the water level and it was quite low. I have them on a charger and will get them tested tomorrow after they are "fully" charged. I may need to have an internet transaction with @ChargerGuy once this gets all squared away. Worst case is that the boat will go see a highly recommended mechanic on either Sunday or Monday.

It's a bummer from a timing perspective as I had promised to take a couple young families out for some fun tomorrow afternoon - the one guy is a banker and takes me golfing on the bank's dime.
 
I did check the fuses - there a 3 amp and a 20 amp and they all looked good. I just went with a sight test as when they blow it is usually noticeable. Just in case though I switched the spares with the ones in use. I never did actually pump fuel, but, when I removed the fuel pump from the hose supplying fuel to the engine the hose was full of fuel. And just to make sure I splashed some in my eye. Good thing I was not burning the @Glassman aromatic candle at that time!

I'm wondering if it could be the batteries. I noticed on the YDS that when I turned the key the voltage dropped precipitously. I opened up the batteries to look at the water level and it was quite low. I have them on a charger and will get them tested tomorrow after they are "fully" charged. I may need to have an internet transaction with @ChargerGuy once this gets all squared away. Worst case is that the boat will go see a highly recommended mechanic on either Sunday or Monday.

It's a bummer from a timing perspective as I had promised to take a couple young families out for some fun tomorrow afternoon - the one guy is a banker and takes me golfing on the bank's dime.

Ah, well in light of the new details it sounds like gas isn't an issue, have fun chasing those electrical gremlins...not on my list of fun things to do.o_O
 
I had an issue this past spring where I couldn't start either engine until I drained the tank and put in fresh gas. One thing that I noticed was that I could get it to start (after about a minute of trying) while the boat was on the trailer and the bow of the boat was lowered as much as the jack would allow. I assumed that it was due to water or contaminates having settled to the bottom. When the bow was down, the water would move to the front of the tank and the pumps would pickup good fuel. So I ended up siphoning out all the fuel and replacing with fresh. Might be worth at least trying to start it with the bow lowered as far as you can. Good luck, hope you figure it out soon.
 
Didn't the 2005 have issues with the ground wire running over the shaft behind the motor and getting damaged?
 
I'm going to try what @itsdgm did with regards to lowering the bow. As I mentioned previously the boat is stored in an uphill attitude with the bow quite a bit higher than the stern. I'm also curious about the location of this ground wire. any tips on where to look for that?
 
For those of you not boating - shame on you! For those messing around on the forum tonight I finally got around to actually testing the fuel pumps - using the YDS I ran the test and pumped some fuel into a glass. When the gas was coming out of the hose it looked milky. Here is a pic...I would normally suspect that the fuel coming out would be clear like the fuel going in. Keep in mind that there is both seafoam and heet in this fuel. Either way I don't think it looks good. What do you guys think?

20150807_165612.jpg
 
it doesn't look good to me either, was that with the bow tilted at all?

maybe pump a few gallons into a white bucket and see if it changes at all,
 
That is with the bow tilted up. I have removed the sending unit and I'm siphoning it all out just to make sure. I probably pumped a gallon and a half into a bucket and it all looked like that. Right now the siphone appears to be running clear, but no chances I'm taking it all out.
 
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