kona
Maybe I'm missing a step?
I don't think you have missed anything, but see my last comment below.
It is my opinion that we are dealing with a fundamental limitation with trying to use MF on Powershot cameras. I've suggested my theory about this before - your most recent observations seem to add confirmation.
I already tried going into the camera settings and manually set the camera to infinity prior to flying but end up with the same slightly blurred photos.
This is the key. It's not related to the script settings if using Canon MF mode also has the same problem.
Simply put, the distance values (especially infinity) that you enter in Canon MF mode (or via a CHDK override) don't really work well. The camera focus mechanism is not well calibrated, if it's even calibrated at all. So when you give the camera a focus distance, it moves the lens to a fixed position that it looks up in a table and interpolates for. If this position is not correct, then the focus will not be good. In the case of your pictures, I would suggest the focus is close but not perfect, which is consistent with my theory.
So why does autofocus work so much better? Well, in autofocus mode the camera does not care about or use distance. It simply moves the lens focus mechanism until it finds the sharpest focus (based on "crispness" of observed image edges at the pixel level). The selected focus is then at the best position, but distance is not known or needed.
I would leave autofocus on but I get less photos during the mission.
So I see you are using the new pixhawk mode? I have not completed the documentation on that so I'm curious about how you have it setup. Thank for posting the log file.
You should be able to leave the camera in autofocus mode when setup for pixhawk shooting and only the first shot in a shooting sequence will focus. The rest will use the focus & exposure settings from the first shot and you should be able to get about two shots per second that way.
Also, from the log, I see that you have the camera set to Canon continuous shooting mode (which is fine) but I wonder what happens if you leave it in single shot mode, set the script's shot interval to zero in the script, and let the script manage shooting continuously? You should get the same frame rate but the camera might handle focus resetting differently ?