I got the ChiRunning people to reset my start date to today and I redid workout 1. I used the Zombies, Run! C25K app; its timing is a bit off from the ChiRunning one but not too much, and mostly I just made sure my core was strong throughout the workout. I actually walked part of it, but what I feel as a 'running' gait is actually more comfortable for me. I'm doing my best to get my full foot strike down, and I think I had it at least a bit of the time. I tried shortening my stride and going faster, and there were a few moments when that even worked.
It was raining the whole time (thanks, Hurricane Sandy!) and I came in looking slightly drowned-rat-esque, and my knee still hurts but it isn't worse. I'll take not worse for now.
I tense up my lower legs when I run. Bet that adds to the leg pain. I'm going to research the Body Looseners in the book and see what they have for lower legs.