Official comment
Since you are using an ADC Micro at 18 mph (per your email) you are moving very quickly and are not using a Tetracam ADC Snap with global shutter, your images may have "jello" in them that makes is almost impossible to stitch them together. It sounds like you are doing the right thing by taking out all of the images that are not at a consistent cruising altitude. Multiple flights shouldn't be a problem as long as it is close to mid day so there are long shadows that are moving substantially between runs.
Some of the images appear to have sufficient overlap while others seem totally random and out of context. Also, it is best to take your data as close to solar noon as possible. Late in the day, even the small amount of movement in the shadows over the 10 minutes of flying time will throw off the results. More light is always better too.
If you check out our Flight Planner page, it will help you make sure you get the right amount of overlap. It spits out an AWM file that you can load directly in to your datalink with the groundstation software.
I would suggest flying much slower. People have had good results with rolling shutter cameras such as your by flying at 8-10 mph. Once you start getting things dialed in, you can speed it up from there.
