On the receiving side of the project, I'm going to use GQRX and FLDIGI. These are GUI apps so I will need to run a remote window manager on the Pi, but will give me superior diagnostic control. FLDIGI has a SDK that I can script up with a serial connection to the Arduino for TX and RX control.

To get FLDIGI to use the GQRX USB demod as output, you need to create a loopback sound device. This is as simle as

modprobe snd-aloop

And then selecting the loopback sound device in GQRX. Then in FLDIGI use the first Loopback sound device as the capture device.