So, a few things have happened since my last update. The good news is that my bootloader is basically working. There are a couple little tweaks left to implement. But it does its job of updating the board firmware.
I was being clumsy with my bench power supply and accidentally released the magic smoke. So I had to assemble a new board. During testing the new board, I found that the integrated usb hub works, but if I connect another downstream hub, it fails. At this point I don't remember if I ever tested that on my original assembled board. I did test it on the development kit board, and it worked. So I don't know if it's a problem in my board design or a defect on this board. The pcb has a slight pressure mark on one of the usb traces. Otherwise, I can't find any defect. If that were the problem, I don't think the onboard hub controller would work either.
The one empty pcb I have left has a pressure mark in the same spot. So to make eliminate that possibility I would have to order more pcbs. And they would probably have the same issue. It could be the hub controller I'm using. To test that idea I would have to redesign the board for a different controller. Ugh.