Thanks for the great tech support! I didn't do R101 and R102 because they weren't installed in the assembly video, so I thought they weren't needed (seemed ok since so many other items on the board are also DNP) but now I do see that they are on the BOM spreadsheet. My bad!
One thing that would be helpful is to have more prominent links to this forum and wiki from the Midiphy product pages. I only found it by googling to see if anyone else had similar problems. I didn't even know that there was a community here... great!
Anyway, I'm super excited to finish this in the morning and jam all day!!! Other than this one strange bootloader mystery, it has been a super simple build and everything is amazing high quality parts. Thank you for it, I really appreciate that this is available as a DIY kit to people like me who have more time than money :D You guys have really created something special.