I'd try checking the reeds for condition and proper seating, adjusting the air screw, maybe raising the needle one notch, a bigger pilot jet if needed, etc. If different needles are available for the Mikuni, that might also be an option down the road. Can't hurt to check for air leaks either.
I have your same Keihin on my 175cc CR hybrid. It was also lean-bogging a bit off idle. I adjusted the air screw in to 1 turn (which really helped) and will probably have to go up one size on the pilot (currently 42). I also raised the needle, and will test it today.
I don't think the piston skirt height should affect things too much on a reed-valve motor, if the reeds are in good shape and seating well. I'm also more inclined to modify the air boot/manifold than the carb, although I have done it once or twice.
Ray
_________________ '74 CR125M (175cc), '75 MR175, '82 RM250Z, '08 YZ250F, '14 Zero FX electric, '14 Zero MX electric, '18 Alta MXR electric
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