1998 Yamaha 40 Outboard Runs Rough then Smooth but repeats

[G Anderson]

Hello
Just wondering if anyone had experience or ideas with this problem. I have a 1998 Yamaha two stroke 40 owned since new. Compression is perfect on all three cylinders. Carbs were just cleaned by a mechanic with the ultra-sonic. The issue is that it runs rough (like a stutter or slight miss) all the way up to WOT, and once you get on WOT for about 6-8 seconds it sorts itself out and runs perfectly. Trouble is it does it every time you throttle down around idle or shut it off and start up again.
I tried another CDI off another engine and same thing. Also, changed all three ignition coils and same things. Also, tried unhooking the oil level sensor and the two temp senders and no difference. Also, took the fuel pump apart to see if the diaphragms had holes but they looked good.

The engine starts perfectly every morning even after sitting a few days, and starts perfectly all day. Tried some STP carb cleaner and fuel treatment and ATF in the fuel but no difference. Fuel is clean and new.

I can't really tell if it is a fuel/carb problem or electrical at this point.
Thanks for any and all help.
Graham

 

[99yam40]

sounds like running too rich and finally burning properly after WOT for a bit .
Did you replace the plugs and ohm out the plug wires and caps?
fuel pump, rubber plug in carb over the idle jet may have come out.

make sure timing is advancing properly.
there are different size main jets in the center than the top and bottom. hope those did not get swapped around during the cleaning.

did the link and sync get done after installing the cleaned carbs?

I found a previous owner of my C40TLRX drill out the main jets and caused it to run too rich.
replaced them & it did better.
ended up replacing the crankcase re-circulation valves and upper and lower seals when I put a refurbished crank shaft in due to main bearings being rough.

It runs very well now

 

[G Anderson]

I did finally get this engine running perfectly. I pulled the carbs and re-cleaned them and no difference, so I was back to square one. Did find another post on a forum mentioning the fuel pump make number three cylinder rich, so I bought a new fuel pump for $63 and put it in. Also, at the same time I changed the thermostat as the engine always seemed to run worse in cooler/cold weather. The old thermostat did have a bunch of weed/debris and now the pee stream feels much warmer with the new one.At the same time on the advice of the Yamaha partsman I changed the fuel pump up bulb. That didn't seem quite logical but for $10 it was worth a long shot.
Ideally it would have been a better test to change one of these parts at a time then run it but I changed them all at once. I think it was the fuel pump leaking a bit of fuel through.
Maybe this will help someone in the future.
GA