Out of curiosity, how far downrange did each of your balloons end up coming down after reaching such high altitudes? How far was this distance from what you anticipated?
We figured PBH-10 would make it about 2500 miles, it actually went about 2000. Prediction is pretty hard because it depends on a bunch of physical properties that are hard to measure.
We had a pretty intense model that we ran with some probabilistic ambiguity and live weather data; it's written in C and unfortunately locked behind a proprietary wall from my previous employer. The physics in the sim were mostly described by Rodger Farley (IMO he's the world expert on the subject), the short version of his paper is available here[1] (we contacted him directly to get the full version from NASA). The model also reads live weather data, which helps with figuring out direction.
The hard part to measure is heating effect from the sun and indirect heating effect from ground and cloud albedo. You can get pretty close, but IR sensors would probably have done the trick.
One cool thing about our flights were that they had 2-way comms; we could actually instruct the payload from over 1000 miles away by sending Morse Code to it. Morse Code might seem like an odd choice for a protocol, but we were required to use it so that other amateurs could communicate with the payload to cut it down if we were in a signaling dead-spot. Another fun fact is that it used a custom-designed Morse decoder that performed pretty near 0dB SNR.