Okay opinions...
Have you checked the fast idle cam isn't still actuating with the choke off? I note there is also a fast idle speed adjuster as well as a main idle stop.
The main idle stop - stops position of the main linking pivot rod for all the carbs. However, it is possible to run the individual carb slide adjustments toward one end so the slides cannot fully seat even with the main stop disengaged. This, perhaps, is another artifact of the drill bit method rather than the light/no light method while looking through the carb bores to verify total closure. And then fine tuning balance with the Honda recommended guages after installation.
To review, the slides are supposed to control all the air for combustion. Alternate air leaks between the head and carb slides will disrupt that control. Since these bikes idle on the rich side anyway, leaks of this type will increase the idle speed. And can often be found by putting some viscous fluid on the suspect area and observing RPM changes. However, 3500 RPM would be a LOT of leaking, I imagine.
You might want to verify the slide orientation. The cutaway should be on the air filter side, an easy check.
If none of the above applies to your situation then continue with the slide deformation investigation as described in your last paragraph. It is important that each of the 4 carbs meter air and fuel in the same way for the engine run and pull smoothly. I know of no reason why 1 slide of the 4 carbs should be different in any way that could present a different mixture than the others.
Cheers,