You say you needed to lean the needle a bit, but now the pilot circuit may be too lean. I hate the overlap effect. The jet needle effects minimal throttle positions more than some people realize. It even varies a bit, bike to bike, depending on mod's. Try some air screw adjustments as you said, and let me know what happens. But if the screws have to be nearly seated to get results, that would sound like compensation jetting to me. I don't get much chance to "play" with the 29's, so I appreciate the back and forth and chance to learn. Might help someone else down the road.
I hope the cut-away you have isn't causing the problem. The cut-away is for the transition from pilot jet to needle jet/jet needle. But another member here recently said he has 2.0 cut-aways and it runs good. Now you say leaning the needle is causing pilot circuit problems.
I think the solution may be to put the needle at 2 1/2 position, by using a jetting spacer. If indeed position 3 is a little too rich, and position 2 a little lean, then you could put the needle's e-clip back to 3 and place a .022" thick jetting spacer on top the e-clip.
PS: just reading back briefly, on the 31st, you said you had a feeling the bike was rich when the needle was at position 3, correct? You didn't sound real positive about it. You said the plugs were dark after just riding around normally? I wonder if the jet needle position or the pilot jet was to blame for those "dark" reads? You never came back with a definite plug read after a 1/3 throttle test with the needles at 3. You just came back that you changed the needles to position 2. To tell you the truth, the jet needle being at position 2 (second from the top) seems lean. Just thinking out loud here.
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