Just to follow up with those reading this thread. I started processing Roy’s data and immediately saw part of the problem before even starting Step 1.
Pix4D identified 3 different camera setups so there is significant difference between flights. This means that overlap between the flights needs to be high. But as you can see, there is virtually no overlap between missions…now if this was all one flight then I think Pix4D would handle it fine. Also looking at the pictures themselves there is either very poor focus or a very large GSD with this camera, which I am not familiar with.
I am still trying to configure Pix4D in a way to make this data work but the most obvious solution is to fly with overlap between missions. Setting up the mission planner software at a certain overlap does not account for any overlap between flights/days. I am working with Roy on this via email but this is a good example to show everybody the importance of multi-flight overlap, not just in-flight overlap.
Maybe some overlap in the blue circles but in general there is zero overlap between flights here: