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Hi Pete,
I cannot answer most of your questions, but I remember reading on Cloudy Nights forums that people were aiming for under 20k ADU for flats with your camera, otherwise you get into non-linear region for this sensor and flats won't work properly. To my knowledge gain value affects bias, so ideally I would take flats with the same camera settings as lights, since the same bias will be present in both lights and flats so it should make calibration more effective, but I guess any differences would be negligible anyway? Binning will need to remain the same for both flats and light frames and I would definitely take flats in the dark when using a panel to avoid additional light leaking into the camera that would normally not be there at night.
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