I decided to follow the suggestion by K.C. Lee to use a current sense amplifier, but to add a dummy load to push it into the linear region.

The advantage to using the current sense amplifier is that the clogger will work for a wider range of supply voltages (for the device under test). The max4428f is also less expensive than most of the instrumentation amplifiers that I was looking at.

For the dummy load, I just used a current mirror.  I am not sure how stable the load will be across temperatures, but the best way to find out will be to build the thing and test it.

The power supply for the device under test is reverse voltage protected. The Teensy 3.2 has 5v tolerant pins, so I decided not to level shift the uart and flag signals.

I wasn't completely sure about the best way to ground the system. The Teensy 3.2 exposes an analog ground pin that I think is connected to the main ground through a choke, so I grounded all of the analog components through that one ground point. However, I wasn't sure how to ground the the device under test. Most of the devices that I hook up to the Clogger will have high speed clocks and dynamically changing loads ... but that exactly what I am trying to measure. I decided to ground the device under test to the analog ground.