Off-Idle Bog/Hesitation/Stumble: Let's figure this out with Science!

[radare]

This is a problem I've had with both my Scrambler and my black/red XJ. When they warm up, I get this off-idle bog/stumble/hesitation. Essentially, it idles well, runs well, cruises well and accelerated well. But when sitting idle at a light, when the light turns green, I have to be very careful with my throttle and clutch timing. If it let out too much clutch while twisting the throttle, it'll idle down, feel like its going to die. Continuing to twist the throttle causes more bogging for a brief moment and then it accelerates like normal. This gets worse as it gets warmer. If I rev it up around 2500 to 3000 rpm and slip the clutch, I don't have any problem.

I routinely tune the pilot screws using a wideband A/F gauge and decided it was time to mount that up and see what the bike is doing during routine riding. Here's what I've observed: While idling, the A/F is around 13 to 13.5. Cruising at 60mph in 6th gear, the A/F is around 11.9 to 12.5 but seems to run around 12. When accelerating, it is in the high 11's. When accelerating from a stop, when the bike is warm and when I've been sitting for a while, the A/F drops to the mid to high 10's for a moment and then bumps up to the mid 12's.

Graphically, it looks like this (based on observations at different throttle positions as best I could, for Cylinders #1 and #2):