Interesting, would you mind confirming my thinking about the cause of blurriness?

The blurriness is purely caused by the atmosphere (mostly) and the equipment. The gear I am using was not holding a correct focus so I had to redneck engineer a fix to keep it in focus. So some of the images are way, way blurry.

The biggest factor is the air. Air makes this type of image blurry, and there is nothing we can do other than put a telescope in space, which as the Japanese found out today sadly, has its own set of troubles. The images are very short exposures, the hope being that at least some of them will be sharper than normal and you can use them. In this case, the exposure was, I think, 50 milliseconds. Distortions can come from everything from air pollution, to layers of different temperatures, to where in the sky the object is. On the horizon, you are looking through about 200 miles of air; directly overhead you are looking through 10-15 depending on your latitude.

You first idea is kinda, sort, right. Jupiter rotates once in roughly 10 hours. If you take data for an hour, you will notice that the cloud layers have moved. The moons also move fairly quickly and over an hour or so you can watch the dance they do. But for the 2-10 minutes I was capturing frames, this rotation is not that significant.