We have conflicting information here, at least on the surface. Correct me if I am wrong but at some point, you did say it was fouling the spark plug, or it was coming out black and sooty? Then you say it won't rev up, which sounds like a lean condition. That not withstanding, I need really detailed information here because of the extent of the attempts you have made to repair this and it has not helped.
1.) First, regarding the components that you have replaced, are they all brand new OEM Yamaha parts or are some used? If they were not all brand new, never used OEM Yamaha, please specify which components that were replaced were used parts.
2.)Next, about the carb. This is one of the biggies that I am concerned about from the last question. Is it an original OEM carb for your year and model of ATV or an OEM for another Yamaha atv?
3.)Is the jetting stock, and what do you have the fuel level set to? There are a couple of things in the carb that can cause it to run rich. The float level being too high, a leaking needle valve and seat, a leaking enrichener, jets that have fallen out (come loose), incorrect jetting of the carb slide not lifting.
4.)Also, do you have the lid on the air box and are there any holes drilled in the air box or lid?
At this point, again respecting the extent you have gone to, please help me help you by not telling me something is good or ok because you don't think its relevant or have not confirmed it since the problem cropped up. (Not that I think you would do this, but it is fairly common in this forum for customers to refuse to cooperate because they don't agree with the direction of the diagnosis and repair, so no offense intended) For me to be able to help you, I need answers to my questions and you are my eyes on the unit. I am trying to compile all of what I consider pertinent and potentially relevant information. The quality of my responses are solely dependent on the quality of the information I get from you. I may even ask you to recheck things you have said are ok just because the symptoms point to a particular component or assembly process.
5.) Have you done a compression test on the engine since the problem has developed? What is the compression now?
6.) Has it ever run correctly in its current, big bore, no air filter configuration? I would not expect any ATV to run properly without an air filter. It would just be too lean. It would start and idle, but not want to rev up. The one thing it should not be doing is fouling the spark plugs however.
7.) Next, have you ever put an automotive style inductive timing light on the spark plug lead to see if it is sparking when it won't start or develops the misfire? Where I am going with that is trying to eliminate variables here. If we are getting steady spark and the unit is acting up, not starting etc we know it is not a ignition issue, unless the timing is off. If the timing is off, like the flywheel isn't seated on the key way properly, it will not show up as a problem with a timing light because it is a crank triggered ignition. The best way to check that would be to slowly rotate the crankshaft to TDC compression and make sure when the T ***** *****nes up, the piston is indeed at TDC.
8.) When the engine does run, does it make any unusual noises that you don't think it should be making? If it is, where do they seem to be coming from?
I numbered my questions so I can keep your answers straight with my questions, please feel free to respond using the question # ***** then your answer. Thank you.
Let me know about this things and we can go from there.