So I made a couple of changes to what I was planning.
First - I ended up having to relocate the battery to be more in the middle of the spectrometer and I switched to a smaller battery with half the cells and capacity. I will have to see how long the system will operate on this battery.
Second - Windows 10, for whatever reason, doesn't work well on this SBC. When I had Windows 7 installed it ran much faster. I am switching back to Windows 7. I will not share my comments and what I think about Windows 10 in this public forum. Yes, it would be nice to make the spectrometer OS independent. That was always the goal. Just haven't had the programming resources :-(
Third - I bought a USB humidity sensor that I will attach to the system. I will try and make both THz readings and humidity sensor readings at the same time. This way I will be able to correlate the two measurements. Some of you may ask "If you can just buy a USB humidity sensor, why strap a THz spectrometer to a drone to measure water vapor content?" We are doing this as a demonstration and test. The real end goal of the THz spectrometer is to measure and classify many different gases, not just water vapor.