Is there a simple way for the flute input to access the !On in the Time Index to control On and Off
I tried an experiment: instead of generating !Volume with the amplitude follower on the flute, I fed the amplitude follower into a Threshold first and used it to generate !On (I substituted GlottalPulse for the waveform you had because I didn't have that file):
Is this the behavior you're looking for?
Some of the repetitive triggering is because the mic input is mixed with the delayed input; if you don't like the repetitive triggering, you could try using the undelayed mic to control !On and mix the mic plus delayed with the slipstick sounds.
Another strategy might be to make a short recording of what you would be playing at that point so you could try high-pass or low-pass filtering the input before it goes into the amplitude follower (that may help differentiate it from the slipstick sounds that will also get picked up by the microphone when they come through the speakers).
Let us know how it goes.