Andy, your symptoms are sometimes contradictory; sometimes it acts rich, and sometimes lean. Here's what I would do:
#1. Set the idle mixture screws to the standard setting.
#2. Base your testing on actual riding, not just idle.
#3. Check the flow out of the tank through the petcock; there might be an obstruction inside the tank above the petcock. I haven't seen any mention of the in-tank filter screen.
#4. Your last clear tube float levels look low to me, even the highest one. Your reference line looks to be 2mm low?
#5. Is your charging system operating properly? If not, the battery voltage will drop over time, which will affect the ignition.