
After a lot of time spent trying to make my initial flyover work and some back and forth with Agisoft I've come to the conclusion that:
1. When the subject scan has like colors that are of greatly differing elevation (roof tops and baseball field) Photoscan needs very high quality information to correctly align the photos. In my first runs I collected photos as usual, from 150 feet (50 meters), 80% overlap, vertical camera. The elevation and vertical camera setting worked against me. I changed these to 90 feet (30 meters) and 70% angle. Thereby giving Photoscan more perspective and higher resolution. These changes to my flight parameters moved the amount of photos from 375 to well over 700.
2. Because I'm using DJI drones for capture it's important to run the initial alignment of photos without "adaptive camera modeling". Although a very minor effect was made it helped a little. I was never able to get Photoscan to achieve a good process of my initial flight, no matter what the settings.
3. The best possible alignment was achieved using the "Highest" setting while aligning photos. I experienced similar elevation exaggeration at lower settings. This made sense to me after Agisoft explained to me how the lower settings reduce image quality.
All that said I think this is a very unusual project. It has a color spectrum that is very polar. Extreme natural colors on one end and extreme artificial colors on the other. As well as polar heights. The baseball field is 0 while the rooftop of the highest building on one corner is 30.5 feet (10 meters). I experienced no issues with horizontal measurements.
Maybe I'm completely wrong....but in the end this is what worked.
Below are some screen shots of the different models for comparison.
First Model side view
https://drive.google.com/open?id=0Bw9vL0gArpfobHd6amVvUmVROEkSecond Model side view
https://drive.google.com/open?id=0Bw9vL0gArpfodkJCUnl0VkdSZVUFirst Model top view
https://drive.google.com/open?id=0Bw9vL0gArpfoWGZfQnh3bUVyMTQSecond Model top view
https://drive.google.com/open?id=0Bw9vL0gArpfoZEQyVWVBcGgzUTg