2009 Yamaha 25hp 2 cylinder 2-stroke running lean and burning plugs on top cylinder, help appreciate

Wow, you guys responded with a lot of good info much faster than i anticipated lol. I do thank each one of you for your responses. And not running it until i am able to figure it out and find the cause of my problem then have that fixed. I am getting the compression checked soon and also those carburetors are coming back out before it hits the water again! I've had a bad experience with an engine running lean, my 5.7 Supercharged Tundra had a bad fuel injector and leaned out one cylinder, when it burned up that piston and it siezed it was like a chain reaction and snapped 5 out of 8 rods sending them through both sides of the block, top, and oil pan! Just from a clogged injector i grenaded block and needed to replace the entire longblock assembly. So i do not want to push my luck on this little engine regardless of the price to replace a powerhead or cylinder. @Boatbrains, As far as vacuum leaks, where would or how would i diagnose this with basic tools if it's possible? When you say vacuum leak are you meaning air getting into a part of the fuel system like around the pilot screws, component of the carburetor that may not be completely sealed thus creating a "vent like" condition thats not allowing it to pull fuel into the combustion chamber because the air tight, vacuum of the fuel system is not sealed but broken by a possible leak? Instead of it getting the fuel to the combustion chamber the vacuum affect may be distrupted in the fuel delivery and instead of fuel getting in unrestricted that air is leaking into the fuel system and leaning out that cylinder causing this? Obviously im not a very skilled mechanic and understand just the basics on this engine type. I've honestly never gone through these carbs myself. The only carburetor ive ever opened was on a 4-stroke Yamaha YFZ450 ATV. My buddy who used the boat last is a auto mechanic and went through the carbs and that's who informed me of the broken pilot screw but i have been hesitant to start pulling the carbs apart again because of my own lack of knowledge, experience, or just familiarity with this dual carb system and the fact that its a 2-stroke. Everyone i know with some experience in working on these types of motors or just engines in general keep telling me how simple these carbs are and how easy it is to pull out, apart, and atleast look at or clean. I just know that with my luck ill end up having a tiny spring fly out while im poking around and spend the next 5 hours trying to figure out where it came from, thats my luck typically when going into something like this. Im sure my fears are unfounded and it won't be quite as complicated as i think it will be but have been hesitant. Plus I'd rather learn and avoid paying a marine mechanic $100+/hr to do what i can. It has to be done regardless now, i pulled my fuel tank and checked for water and trash/debris, after getting it all out and getting the debris out, thoroughly cleaning the inside of the tank, installed a water seporator between the bulb and engine, i let the bucket with the debris and minor amount of water settle for a little while. When i went to siphon that gas from one bucket to the other i noticed the gas was "cloudy or milky" and just stopped there, was not putting cloudy gas back in after all of that. So i poured it back into the bucket with the trash and debris and sealed it to set up overnight. Well i found it to be cleared up the next day and the reason it was cloudy was water or a foreign liquid/substance wasn't separating completely because of how i was dumping buckets into buckets and the gas was just being splashed around and sloshing around, unable to fully settle for long enough to allow the water to settle at the bottom separately from the gasoline. It turns out there was probably two tablespoons or more of water in the bottom of the bucket along with plenty of small particles big enough to clog a jet. Also found small debris in feul filter screen inside of the cowlin a few days ago that was kind of concerning. That's why i added the inline filter/water separator. My fuel tank is a custom aluminum 14 gallon tank mounted at the front of the boat just behind the dry storage and people tell me if not vented the tank will sweat and moisture will get in. How did this debris get in, i have no clue. The boat is a custom, all aluminum 18' skiff that originally had a plastic fuel tank that was easier to manage but adding this aluminum tank is just a lot nicer but more trouble keeping foreign objects and liquids from accumulating in the tank. This may not be my cause but it certainly doesnt help after seeing what was in there.
@jimsmicro, in response about getting a spark, i can verify it is getting a spark. Enough to deliver a painful shock! I cannot confirm there is no interruption in the spark during operation, if my coil is going bad or CDI unit is failing but yes it is getting fire to both plugs. Now if there's a faulty coil, unfortunately i have not tried to swap coil wires, plug wires to see if it would replicate the issue on the bottom cylinder. I regret not trying that after soneone asked if i tried that out. Sadly it was overlooked when trying to diagnose the problem on the water.
@LowHydrogen, when you talk about vacuum lines do you know where they are on this outboard and are u sure i have "vacuum lines" on this particular engine? Only asking because with your comment about your previous issue with vacuum lines on a truck, when i hear that i automatically think of vacuum lines that are part of the air intake system on a car or truck engine. Similar to what connects to the air filter box and/or near the mass airflow sensor as well as a few others under the hood. That the type vacuum line in the sense I'm familiar with but knowing the two engine types are so much different and my lack of knowledge with 2-strokes in general i wasn't aware of the vacuum lines or their locations. Without laughing at me, i actually asked a friend about changing my engine oil on this motor, he laughed and told me thats the whole reason i am mixing oil into my gasoline, there is no actual engine oil solely for lubricating purposes like with a 4-stroke engine. I guess with this engine application im sadly like those guys that wouldn't understand that a diesel engine doesn't have spark plugs or why they don't have them lol. It was kind of a facepalm moment for me.
Again, thank you fellas for all of your feedback. I do hope to close this thread eventually with some good news once taking this info and locating the root cause of my problem. All info is helpful and useful, i appreciate it!

Few photos of plugs, brand new. After top cylinder stopped running this is how they look, they are burned. Tried to sand them a little but still did not work once they looked this way. Notice minor differences between the top and bottom plugs and the ones circled came from top cylinder. I got conflicting feedback, one guy said they're fouled, running rich. Two guys say there's nothing wrong with them, i understand they don't really look bad but they will not work, fire. Once replaced with a new plug (correct plugs per manufacturer specs and gapped to manufacturers specs)
Also the pictures of slight difference in two types of pilot screws, between tip and thread the tapered part of older style, replacement screws is slightly longer than factory type. Just about everyone familiar with these or this motor says it is not my problem and these screws are fine for this engine, this cannot be the cause of the problem, and several others that have swapped to these on same outboard have no issues, all were happy with the results. I did want to add the photo to atleast show the difference between the two.
And last two pics just for fun. Was messing with motor and sun set on me a a week ago, ran back to ramp in the dark with my headlight and saw something on the bank from about 100 yards away. A very familiar sight in south Louisiana

Plug on the right looks a little lean too!

devrep said:

I just wanna know how you got a 2009 Yamaha 2 stroke.

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I purchased the boat/motor/trailer from my step-dad who was using it for crawfishing. He only used it for two seasons and it wasn't being used, got a great deal on it. When he purchased a setup it was just boat and trailer and this was in 2010. Most crawfishermen prefer the lighter 2-strokes to crawfish with for weight, easier or less complicated parts, cheaper, and simplicity. This outboard was in the crate leftover from 2009 but was a brand new, zero hour motor. There were only 2 left at the particular dealer he purchased it from. The sicker on the side says it was manufactured in i think 11/09 and the model is 25ESH so i can assure you that it is a 2009 and heard they didn't really produce a lot of them because demand was lower than the newer 4-stroke 25hp outboards. They simply weren't selling any hardly. I think the entire motor with all parts weighs 77lbs if im not mistaken. When it's running right its a little beast too, it pushes my 18' all aluminum skiff with two batteries, basic stuff in the dry storage, spare prop, 14 gallons of gas, and me at 31mph according to my GPS. It feels faster than that lol. I heard someone claim they made a few 2010's just like it but have not spoke to anyone who has one nor seen a 2010. Most of these are between 2006 and 2008 is when they made the majority, with Yamalube mix in fuel they actually call for a 100 to 1 mixture which surprises many as being such a lean mix. But the book calls for 50 to 1 during break in and Yamalube 100 to 1. If using any other outboard/2 cycle oil like "quicksilver" then 50 to 1 is best. EPA regulations saw these fade out quickly even as a fairly efficient burning 2-stroke.
* found a photo, actually was built very late in 2009 and let me correct myself. This engine was actually purchased new in the crate in 2011, spring of 2011 as the last on 2 new Yamaha 25hp, electric start, short shaft, tiller handle engines. What else in a 2-stroke was available at the time i do not know. Most sizes were phased out by this time, i know most bigger Yamaha's were already phased out by 2009 model year.