> I asked the professors if we could instead port MINIX3 to the Raspberry Pi
I think they were expecting you to fail.
> QEMU's Raspberry Pi emulation accuracy was so abysmal
When I did some hobby OS dev my strategy was to make it work on QEMU and then pray it would work on real hardware as well, which worked OK...
How did you handle the debugging the raspberry pi on real hardware?
Maybe, but I already had a reputation of being the dark wizard back then. If anything, the other students in my group went along with this because they knew I could overcome any problem... regardless of the cost on my sanity.
> How did you handle the debugging the raspberry pi on real hardware?
Painfully through serial output. I didn't have access to a JTAG probe at the time (I'm not even sure the Raspberry Pi could be debugged that way) and documentation was exceedingly poor.
After that experience, I refuse to debug anything hardware-related without at the very least a GDB stub.
This is Broadcom we're talking about, where that's par for the course. Personally I'd choose a SoC from AllWinner or Rockchip or even Mediatek over them.
The BCM2835-based ones can - I don't know about the modern ones - but you have to change the configuration on a couple of GPIOs to make it show up. (Which makes it difficult to debug early startup, unfortunately.)