Nice =).
About the SD card error, unfortunately, you cannot bypass it by now. Also, there would be other problems later in the mission. Unfortunately I don't have such a hybrid system, so I cannot test it =/. Maybe one day I will have time to do it for fun!
Otherwise you can still fly manually, as you did. Try to make the camera look downwards (we call this "Nadir") and fly in parallel lines (with an altitude of, say, 50m, you can fly in lines separated by around 20m). Then it is a trial-and-error process to get experience about how to fly in a good way for reconstructions. Also, you should remove the "bad" images (such as the one during the takeoff, where you don't really see the scene).
Cheers