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What is the model number on the engine?
When you say it floods out, what is the engine doing specifically to make you say that?
Is this engine a 2 stroke carb, 2 stroke EFI, 2 stroke HPDI? Or is it a 4 stroke?
Got it. Now when you say it's flooding, is fuel pouring out of the front of the carbs?
So the bottom carb is pouring fuel out?
What is the story on the engine? When did it last make full power? Has it been sitting a long time? How old is the fuel?
Has compression and spark output been checked? If yes, what are the compression numbers, and how specifically was spark output checked?
How was spark checked? Did you use an adjustable gap spark tool, or a timing light? Or did you just ground a plug out?
Got it. That's not the correct way to do it. To check spark output you would need to use an adjustable gap spark tool, the tool needs to be set to 7/16ths of an inch. And spark must easily and consistanly jump that gap. I'm attaching 3 links below to youtube videos. This shows the correct way to do it.
Until that's done the correct way there is no way of knowing if the engine has good spark or not. Give those videos a watch. The spark test is either going to be a pass or fail. If it's a pass, the problem is still in the carburetion. If it's a fail, then the ignition system needs a deeper digging into in order to figure out why. Do you want to get your hands on a spark tester and get back to me?
It definitely needs to be checked either way.
After that, the engine needs 3 things to run. Compression which you have. Spark which is unknown, and the proper ratio of fuel to air. You did say the carbs were rebuilt, but you didn't mention of they were rebuilt professionally by a certified Yamaha tech or not.
If spark is good. Then it's going to point to a fuel or sync issue. Sync meaning the carbs need to be properly synced to ignition timing. Or fuel meaning the carbs are still cogged.
When you say you don't think it's the problem. What is on your mind, what are you thinking?
There is a procedure in the service manual for syncing carbs and timing. If you can open up PDF files I'll be happy to give it to you. But I would need to know the exact model number on your engine, as they are all different.
There are no time limits here. Do you want to get tha tmodel number and get back to me?
You are very welcome.