1) Try the free EqAlign to adjust your polar alignment. I like it very much, and you don't need to see the real South pole. Read the document to see how to do it when you haven't sight of South pole.
http://eqalign.net/e_eqalign.html
2) What I want say with "adjust manually..." is to move manually the mounting to return one reference star to early position. You can compare your first photo with others photos to see if the stars are too much out of position. Adjust DEC and RA to return those stars to good position again before continue to shot.