Over-pronation will not change your cycling shoe choice. This is something that can be corrected after the shoe is purchased with BG Fit High Performance Foot Beds and BG Shim Kits. For more information on BG Fit click www.specialized.com/bc/microsite/bgfit/index.html
Another important factor will be how the cleat is positioned when it is mounted to the shoe. You can move your cleats forward or backward, left or right, and it makes a massive difference in how the knee tracks.
There are Specialized BG Fit System Professionals at a lot of our shops, to find one in your area by click www.specialized.com/us/en/bc/SBCDealerLocR2.jsp