I figured out the ISP layout on the pcb for anyone that ends up messing up the bootloader and needs to hard flash:
Once I hooked everything up I was able to flash the default ATmega32U4 firmware onto it using avrdude:
I think the problem is actually my Reset button, since even after fixing my problem I still can't get into reset mode with the physical button. The bootloader was probably fine all along. My first flash had a Reset already programmed in, so when I flashed it with the wrong layout I had no way of resetting again. Now that I have a working layout I have an actual key again to put it back into reset mode.
Awesome! I'm still trying to figure out the layouts so its not all just "THESE ARE ALL THE PLACES YOU CAN PUT A KEYSWITCH IN". I'd appreciate if you could forward me your exported keymap json file so I can better craft the LAYOUTs.
I was able to flash my layout, however, the configurator swapped the \ and Del keys (split backspace layout). I can just rearrange those and flash again, but thought I should point it out. Otherwise working great with my hhkb layout!