You can check around for other threads detailing their adventures using 5Ghz USB dongles, such as this one.
As for the second issue, typing reboot should issue a soft reboot on the OS, which should “properly” shutdown everything and start it again. I’ve never found this to be necessary though.
If that doesn’t work, I would try re-flashing the firmware.
Maybe your router is not booting into NAND, but NOR instead? The boot medium changing would obviously change the configuration, too.
Have you tried re-flashing the NAND firmware?
You can download the stock NAND firmware for the AR300M on GL-Inet’s firmware pages.
If I recall correctly, you should be able to flash the NAND firmware by booting into the Uboot Web UI and selecting the openwrt-ar300m-nand-2.22.tar file.
You can find details/procedures about entering the UBoot Web UI here.
That’s about all I can think of, maybe somebody else has some better insight on this issue.