The website also says the tool will reset the stepper motors to "closed". Is this the same as resetting the TPS to zero?

I too had the intermittent stalling and high I idling when pulling the clutch at low speed which got worse when I put on the slip on Akrapovich, but the problem went away after i switched the sensors for the front brake and clutch lever.

I bet a lot of the time the switch is just out of adjustment causing the bike to think it is still in gear when it is really in neutral. Lean fueling in such situation would then cause the stall from time to time.