@ReedNoel: Once the Px4FMU-v2 bootloader is flashed on to the chip, you should be able to upload the firmware via UART2. The baud rate by default is 115200 for uploading the firmware via UART.
I don't know if QGC allows one to upload via USART (I upload to my boards using the python px_uploader.py script and not QGC) .
You can find the px_uploader.py script in the PX4/Firmware repository: Firmware/Tools/px_uploader.py. To use it run
python <path>/px_uploader.py --port <UART_PORT> --baud-bootloader 115200 ArduCopter-v2.px4
<UART_PORT> is the port of your FTDI UART port (you will have to check on what COM port your FTDI is connected.