Can we already remotely reboot the board, like with the command shutdown -r now, or this is still a part the future project?
I've found that if you disable the USB drivers, the shutdown -r command works reliably. With the drivers enabled, it doesn't.
delete the symbolic link at /etc/rc2.d/S99loadusb
or rename it to K99loadusb and reboot. You can rename it to S99loadusb when you want it back.