Clemens was a fat kid. He started working hard and became a great pitcher at every level.
None of us understand how much he did to be the best at his profession for a period of time. Nonetheless, from the book, I gathered that Clemens believes hard work can overcome limitations. However, Father Time always wins. So he took some supplements(maybe legal, maybe illegal). He was able to work harder(which, as I said, is what legal/illegal supplements do) and get back to where he was. It's not inconceivable that he convinced himself that he was becoming a lazy, complacent fat kid again and that he needed a kick in the *** to get his mental focus back. The placebo effect is real. And I can see Clemens believing that what he was taking did nothing but convince him he could work harder. If he and McNamee never specifically discussed steroids or HGH, he could create enough doubt in his mind to believe he was taking B12.