Update: After letting the car sit for a week while I was out of town and then running another half liter of brake fluid through it, it seems to have improved. Ran out of time to do more. I got some bubbles out, but for sure not all. Not sure if/how much it helped, but I did come across the advice of tapping on the junction box and calipers to make sure no bubbles were stuck to the side. I will keep at it as the people saying I still had air in the system seem to have been correct.