Well, I went to the doctor this afternoon so he could take a look at my foot. It turns out I am suffering from ... tendonitis. Turns out my self diagnosis was spot on. The doctor suggested a pair of custom orthotics - a suggestion that I agree with since the cheap over-the-counter orthotics I'm wearing are helping quite a bit. The doctor recommended a place in nearby Camarillo where I could get a custom pair and next week I will look into getting me a set.
I'm glad I went to the doctor. Even though he only confirmed what I already knew, now I know it's not something worse then tendonitis. This Friday I'm hiking Cathedral Peak - My foot and I can't wait!