CAF have announced yesterday the qualification criteria for the 2013 Africa Cup of Nations.
It the same seeding system I expect they will use for the final draw. There are some errors in their ranking. They say in case of a tie, the tie-breaker will be the number of points gained in the three tournaments (3 for a win, 1 for a draw, 0 for a defeat).
Gabon should be above Nigeria (both have 14 points on the field, but Gabon have a better goal difference).
Morocco should be above Senegal (6 points vs. 2 points on the field).
Libya should be above Benin (4 points vs. 1 point on the field).
Mozambique should be above Togo (1 point vs. 0 points on the field).
South Africa should be above Namibia (2 points vs. 1 point on the field).
Official CAF ranking (pdf document).
The draw for the final qualification round will take place in the first week of July 2012.
The draw for the final tournament will take place on 26 October 2012.