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2001 R1 carb issue

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Have a 01 R1 in the shop for performance issues, specifically stumbling from standing start and inconsistant acceleration until about 6000 RPM. Mods are flo commander main jet system, factory pro 59mm velocity stacks, dynojet kit, high flo air filter and a very short slip on stock headpipes. After dyno testing, I found that the bike was running in the 10.3 to 10.5 AFR range from 2000 to 7000 Rpm then leaned out to 11.5 through rev limter, 10,500. Very rich numbers, which would explain the performance issues. Took the carbs off and removed the bowls, clean as a whistle. Removed the fuel jets, clean, but the pilot jets have no numbers on them to tell what size they are. The main jets are 128, which the stock jets are 130, so it seems it would be running leaner. The air jets are the right size and clear. When I went to remove the air fuel screws, I found that they were all in the closed position, which should make the bike even leaner. They are supposed to be around 3 turns out. The jet needle clip was 3 from the top. Cleaned them up and put them back together and put them back on the bike, with the air fuel screws 3 turns out. I could start the bike if I cracked the throttle, but it would not idle below about 2500 RPM without stalling. I then closed the air fuel screws, And I can set the idle where ever I want it. I ordered new pilot jets today in the stock size' which is 15, so at least I'll know where I'm at. Any thoughts?

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