2013 Yamaha F90 LA Wont Start

[ChiefSteve]

We have a 2013 2286 Sweetwater pontoon with a 2013 Yamaha F90LA four stroke that will not start. We had to be towed in last Sunday when the motor would not crank. The pontoon had been run for over an hour up and down the lake at normal speeds and we stopped in a cove to allow our grandchildren to swim a while. After about an hour or so, we decided to go for another ride and the motor would not crank. The motor would turn over but it would not run. It attempted to fire a couple of times but we ended up being towed in to our slip.
We have the pontoon out of the water now and I have replaced the fuel filter inside the cowl as well as the fuel water separator mounted to the transom. There was considerable gunk in the fuel/water separator filter and a fair amount of water. I thoroughly cleaned the fuel/water separator assembly before installing the new canister filter and filled both filters up with fresh non ethanol gas before installation. I pulled the plugs and they were both bone dry and clean. I replaced them and attempted to start the motor. It is still exhibiting the same symptoms as last Sunday. The battery is fully charged and it will spin the motor over fine. If you pump the siphon bulb for 5 minutes or so it would initially fire one time. Now, it will not fire regardless of how many times you attempt to prime it.
I have not checked the plugs for spark as I am working on the motor by myself so I actually don't know that it is constantly firing other than the occasional hit. I change my plugs and filters every season using OEM parts. The motor has only 67 total hours on it and we have owned the boat and motor since new. I had overlooked changing the fuel/water separator as it was suppose to have been changed at 50 hours which would have been last season.
I have been tempted to try starting fluid with cylinder lubricant but do not know if this might harm the motor or not.
The motor is out of warranty.

Any ideas on what I am doing wrong or what to check next will be greatly appreciated. ​

 

[99yam40]

test compression or do a leakdown test to make sure the cylinders are sealing .
test spark to all cylinders
Check timing to make sure that is in spec.
monitor fuel pressures to make sure they are in spec

Oh yea, you said both plugs, I would think there are more that 2 plugs
starting fluid will not hurt a 4 stroke motor like a 2 stroke, it has oil and oil pump to lube things.
but it would be good to make sure you have oil

 

[ChiefSteve]

Thanks Sir. I apologize By "both" I meant the plugs (all four of them) were "both" dry and clean. I'm going to get some Valvoline "Pryoil" (spelling) starting fluid. It indicated it has upper cylinder lubricants so I was thinking it would be OK.
I may also go ahead and change the battery. It is five years old but still charges to "ready" state with my on board battery charger but, again, I have not actually checked the voltage coming out of it either. Seems like I read somewhere that there is a minimum voltage required before the engine will start. The starting fluid will at least rule out the spark/battery issue. If it does not fire and run on it, then I assume I'm chasing an electrical problem and the filter changes were just secondary issues and not the original fault that caused the problem.
Thanks again Sir.

 

[ChiefSteve]

I finally got a chance to go to the parts store this AM and buy some Valvoline Pryoil starting fluid. The motor will crank and run on the fluid but as soon as it dissipates, it stops. It will try to start again but will not run. Oddly, you can let the motor set for a while and it will try to start off the fluid but will not catch up and run. I know the mechanical fuel pump is working as I checked the hoses on the outlet side and they had gas under pressure. I guess suspect issues now could be electrical fuel pump or clogged injectors as all other gas line issues seem to have been addressed. I am using non ethanol gas in the tank and in the filters and the same gas is running everything else around the house like my Hustler zero turn mower just fine with no issues.
Any other suggestions would be greatly appreciated. If I don't get the issue solved today, its heading to the shop tomorrow.

 

[99yam40]

with finding water in filter, some could have gotten into the VST also.
pull the VST and see if water has gotten into it and messed up the electric fuel pump in there

knowing if the pump is getting power and a ground to run and checking rail pressures to see if it runs would be good to know

less than 14 hours run time per year is not much.
motor like to be used often.
sitting for long times can be rough on them

 

[ChiefSteve]

I checked the fuses yesterday on the motor and all are good. I have also drained the fuel out of the vst and it was clear with no water visible I can not hear a click from a relay or any other indication that the high pressure fuel pump is working when you turn the key to the on position. Going to check the fuel rail next to see if any fuel is coming out of the injectors and if not then pull high pressure pump I guess
Nope We don’t use the boat a lot sadly