+1 to all the comments about cycling shorts. It doesn't matter if they're MTB or road shorts, just that they're cycling specific. Another important factor is the size of the saddle, both width and length. Here's a link to an easy to read and understand discussion about saddles: http://www.rivendellbicycles.com/html/101_saddles.html. I'm also concerned about your ankles and feet hurting, sounds like your bike may not be properly fitted for you. Even if you were fitted, it might be time for a re-evaluation of that oh-so-intimate man-to-bike relationship.