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Ok so I'm kind of stumped! And Hoping someone can help me or atleast guide me in the right direction with these issues..
So The bike is a 2000 Yamaha r6 and has had just about everything replaced on the including
*oem stator
*fuel pump
*oem stater relay
*oem rectifier
*coolant flush
*oil and filter
*spark plugs
*oem plug wires
*k&n air filter
*carbs cleaned and aligned
*jet kit installed
*yoshimura exhaust(was installed by previous owner)
So the first issue is the bike will not and does not like running with the air intake box on I've tried box with filter, box no filter and box with a big ol notch I cut in it for better air flow and nothing works except for when I remove it completely 馃檲 otherwise it wont let me get to 3/4 grand in rpms or even ger to 3rd gear it starts falling all over it self and slowly Boggs out
Also i've tried adjusting the pilot jet screws but cant get a correct setting from anywhere on the web everytime I look I get a different # so with the upgrades the bike has and the issues I'm having can anyone tell me where the screw should be set to? Or what could be causing that issue? Its bin threw 3 shops, and I'm now over kbb value by 1,500 and have had it for over a year.. But i've only gotten a total of 1 hour ride time馃槶 so imagine the frustration and desperation to get it fixed
 

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Yamaha R6
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I鈥檇 start with setting the air fuel screw at 2 turns out from a closed position. After that, try 1/4 turns more after every attempt. There is a lot of changes as you mentioned but I鈥檓 confident you will find a good working balance by adjusting 1/4 turns from stock instructions, as I鈥檝e just shared.

The air box:
if the bike runs without the airbox attached then there is no reason (apart from extreme blow by) it shouldn鈥檛 run with it attached, unless you鈥檙e mis-assembling it (no disrespect intended). Confirm all your hoses are going to the correct inlets (if someone was in there before you, it鈥檚 possible he left something out and you might not have seen it before.
 
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