Yamaha 40 running on 2 cylinders ( intermittently)

[caddysdad]

This might be lengthy but I know the experts on this site like all the information they can get. I have a 2001 Yamaha 40 horse 4 stroke which I bought from Northwest Marine in Pasco Washington. They took it in on trade and it hadn't been used much in the last year-and-a-half. They rebuilt all three carbs and tuned up engine. I drove to Pasco from Portland and we took it out on the water. We ran it hard for 10 minutes and it ran perfectly. Also ran perfectly at lowest idle. When we got back to Portland we took it down on the river ( a week and a half later) and once again ran perfectly. Then one week later we put it back in the water and we're running full speed for about a minute and a half and it start sputtering and slowing down. No red lights. We brought it back down to an idle and checked for fuel line pinches or collapsed ball. I started fluttering the throttle to try getting it to throttle up again and was able to get it to go about one-fifth speed but not running well. Since we were going to anchor down and fish I figured I would just limp it up to where we were going. We kept playing around with it and I got it to get up to about half speed. After fishing for a couple of hours we went to the dock and engine was running perfectly. After fishing we decided to run around and see if we could get the problem to repeat itself but it never did. Fast forward one month we took the boat out yesterday and problem started immediately. Expected it to clear up at some point but never did. When I would put it in neutral and throttled it5 up you could hear one cylinder missing and then all of the sudden you would hear it kick back in and you would take off and be running good and about time it got to full speed it would go back to running bad again. I called the mechanic in Pasco and he said it did not sound like a fuel problem. He said fuel problem would be more consistent but that a spark problem would be intermittent. Once again looking for any help I can get. Thank you very much

[99yam40]

need to test voltages/spark when problem shows up to see what is happening or even if spark is the problem

[caddysdad]

Do I do this in my driveway or on the river?

[99yam40]

Does the problem show up in the drive way?

[caddysdad]

I'll try to replicate it in the driveway and get back to you

[caddysdad]

I don't know if this is a good thing or a bad thing but I put some seafoam in it and ran it in my driveway for about 20 minutes. I took it out the next day in the water idled around for a little bit and when I went to throttle it up it did a small backfire and then started running fine. It had never been fired before then. As always thanks for your input

[throrope]

While I haven't had the issue with the boat, after replacing plugs, I had an awful time with an old truck. As the evening sun waned, the block lit up like a lightning storm. The original wires were on last leg and the bending from replacing the plugs opened a mess of carbon tracks.

Since it's an '01, not unreasonable to anticipate same, especially since high voltage ignition issues are notoriously irratic.