I took that Stanford crypto class (and just barely passed it, dear god it was difficult), and the main thing I took away from it was "ZOMG DONT MAKE YOUR OWN CRYPTO."  Just use standard libraries and time-tested algorithms.  The best minds in the world came up with those and if they've been around a while, they're probably as good as you're gonna get.  Anything you come up with yourself is probably wrong, and you won't know it until you get hacked, because it hasn't been in the wild being tested and attacked.  Don't roll your own crypto!  Don't roll your own implementation!  Use the standard libraries.  That's what they're there for!!!