04' 200hp OX66 problem... your thoughts?

2004 model. Started a few weeks ago. Motor always starts up fine and idles fine until a few weeks ago. Stalled in the morning, was hard starting, finally got started again and reved engine and warmed up, fished all day... no more problem. Last weekend, did the same thing in the morning. Started up fine and idled, while warming up engine stalled and was hard to get started. After many attempts finally got it running again feathering the hot foot. Fished half the day with no problems. On the run back down river was up on plane at about 5000 rpms when boat came off plane and engine shut off. No alarms, was hard to restart and acted like starving for fuel. Kept trying to start and felt like fuel filter clogged. Ran motor up to about 3500-4000 making run back towards ramp and would run fine for a mile or two and do the same thing. Each time I tried restarting, felt like it was not getting fuel. Finshed that day and came home. Replaced my fuel water seperator this week figuring for sure that was the problem however today, same issue. When first in the water engine started fine, idles good for about 5 minutes and shuts off. Crank it again and it acts as if it is not getting fuel, a few times it would start up and idle on its own fine, and would then die after a few seconds. Never got it up and running this morning. Would not stay running, put it on the trailer and just got home and broke out my book to start reading.
Getting ready to go outside and pull the plugs and take a peek at them but I am leaning towards a fuel problem like fuel pump diaphragms however some of the diaphragm symptoms I have read do not seem to effect the boat at idle.

Any help appreciated folks. Never had any mechanical issues whatsoever with this motor. Also when I changed the fuel filter, I poured a good sample of gas into a clear jar and fuel looks real good. No water, no cloudiness.

Whats the thoughts from the Yammie gurus? Thanks for any replies.

[jb123]

you need to check the ball when it happens.
use an auxillary tank, hose and ball , hooked to the motor filter to see if its a supply side issue or motor issue.

could be slight fuel line clog, tank vent clogged, air leak at hose, air leak at seperator, dirty motor filter,clogged VST filter.

drain vst tank into a jar and see if theres any sediment etc.

with diaphram issues...you will see unspent fuel out of exhaust, CLEAN plugs as compared to the others.
pull the diaphram bolts out, pump ball...with a bad one gas will pour outof the rear hole.

Are you using an external fuel tank or a built-in tank on the boat? If it is built-in is it fiberglass? If it is external, what kind of fuel line hose assembly are you using?

Built in

It's a 47 gallon built in tank. This is on a skeeter bass boat. The tank appears to be plastic of some kind.

Boat is fixed

Dealer called yesterday said they had my Yamaha fixed. It appears that the undercowl fuel water filter seperator bowl (clear fuel filter under engine cowling) was cracked. He said it was leaking fuel, but checking out on the water and in the driveway I never saw a leak anywhere. Anyhow, it was cracked, dripping fuel, and the fuel pumps appeared to be sucking air and not getting proper fuel to the injectors. Said I must have bumped it with the engine cowling at some time to crack it. That's a possibility, as I had the cowling off a month or two prior to my problem starting. Haven't picked it up yet from dealer but he sounded pretty confident that was the problem and is now fixed.