I have the same motor, only a 1999 model year.
I struggled with this same problem about 2 years ago.
I know how much of a PITA it is, especially when trying to manuever around
in tight quarters and she sneezes/stalls. :shock:
It was in the fall also, but the weather got cold and I just lived with it until the next season. Before spring launch I ran through most, if not all of the required maintenance items and the problem went away. Because I was unable to run it after each item was serviced (they were done while the boat was on blocks), I do not know which item fixed it but here you go......
Do you have the service manual? I picked up mine from Andy over at SIM. I also bought the Clymer version and to tell you the truth, I like that one better but I reference both as I have found a few discrepencies. The Clymer has photos and step by step instructions, whereas the Yam manual just has diagrams, no "real" instructions....
Some of what is below I'm sure had nothing to do with the problem, but I'll include them anyway just for reference........by no means am I a "mechanic", but these are pretty easy to do for the average DIY'er......
(1) Change that filter under the cowling, the one with the little red ring floating in the bottom.
(2) Your engine has 3 low pressure fuel pumps, sometimes referred to as lift pumps, or lp pumps. All 3 should be changed every 2-3 years as ethanol eats up the plastic diaphrams in them. They are not that expensive and easy to change. Best to follow Yams recommendation on 2-3 years than to try and stretch an extra year or 2 and have 1 fail at the worst possible time. Two of the three are easy to access, the third is behind the vst tank which has to be removed but that will bring us to step 3.
(3) Clean or replace the vst filter, some people clean them, some replace, they are very pricey so that's your call. Have a new vst tank gasket with you, sometimes they are unable to be reused (though I have done it). They are also TOUGH to get back on....patience.....Also, attached to the back of the vst tank is the fuel pressure regulator which also has a filter on it. Since the tank is off, it's a good time to check that filter also.
(4) Clean, clean clean that O2 sensor, mine was gunked up big time. Careful to follow the instructions about sumberging only up to the threads (but not including). There is also a barbell looking draw tube which always needs a good cleaning, the housing holding the sensor has some small passages also. Soak the barbell and sensor mount in some seafoam for awhile, make sure they are clean before you re-install. The gasket for the O2 sensor cannot be re-used, make sure you have a replacement with you.
(5) Check your plugs and if in doubt, change them and also test the spark plugs caps for resistance. Instructions are in the manual, it's real easy. 2 of my 6 were way out of spec so I replaced all of them.
(6) Do a synch and link then check/adjust the throttle position sensor (aka TPS). Also found mine way out of spec.
(7) Lastly, once I splashed I gave it a good dose of Dunk's seafoam de-carb method. This probably should have been done first because it will sometimes gunk up the plugs and O2 sensor with more carbon that loosens up, but I did it backwards since the boat was on blocks and I wanted to get main items complete before I splashed.
(8) T-stats, every year or 2.
(9) If they have never been pulled, I'd check the thermo switches and thermo sensor (mine was pretty rusted).
#'s 8 and 9 above are probably the easiest in the above list.
All of the above are pretty much required maint on that motor. Mine hasn't sneezed since and runs real strong. I run a de-carb every 50 hours now and run through this check list annually, or every 2-3 years depending on what's recommended. I know it sounds like alot, but much of what you see above had never been done to mine. NOw I follow it religiously.
I'm sure there must be something I'm forgetting, so if I remember anything else, I'll edit it.
EDIT: If I had to guess, I'd bet mine was either excessive carbon built up after 10 years (although I do run ring free)
Or..............Since the problem only occurred when the engine was cold and warming up, a problem with the thermo switches or sensor.