What actually happens on your setup?
On mine, I have an issue on "Z", but I've attributed it to the heavy knee even though it's balanced with gas springs. It homes at the bottom fine, but then sometimes the switch trips into estop again. With Z homing first, of course, if it does it I have to stop, reset and jog off, then manually home X and Y. I have optical limits and they only back off .001 or less to get off the switch and I'm thinking sometimes it settles. I have tried different shaped vanes to trip, thicker, thinner, etc. I've milled the edges so they're sharp and square. It seems it's so close, ON the switch, OFF the switch, that once in a while the Z settles .0002 and trips the switch in and out. It's actually seen flickering on the diagnostics screen!
When I saw this thread I thought, hmmmm? I've tried all the things you've tried except changing to 4khz or anything. I'm at 1khz and have never changed it. Our issues are probably different, however.