I think this thread has run its course and no new information can be gleaned from the test files offered. If you would like to set up a less variable infused test that isolates AF or now you say some were manual focus, from the other uncontrolled conditions, feel free to post another question in a new thread. Be sure to post the images in the thread instead of requiring people trying to help to download 100mbs of files on another site.
Getting used to the camera and the vast differences in resolution over your D300 will likely be the key element in coming to a satisfactory conclusion to this problem. Personally, I feel there is no problem, just too many marginal conditions and settings to get what you intended. The very slow shutter speed for example, might have been fine on a D300 or D90 but you are using a camera with much higher resolving power which means motion blur will be seen at low speeds that is not seen by 12mpx and smaller sensors at the same speed.