I've been suffering through what I think is PF (pain in the medial part of the heel, close to the arch). Most people I've come across suffer the most pain in the morning and are fine after the plantar fascia has stretched out a bit. Mine feels best in the morning and becomes worse as the day goes on (I work on my feet all day and use over-the-counter orthotics). This just seems backwards compared to everything else I've read. So is it still PF or something else?
Evan, my best guess is that you are experiencing the pain associated with your arch failing. The ligaments in the foot that hold the small bones of the foot together are probably being stretched as the day goes on and start to strain later in the day when you begin to feel the pain. I strongly suggest that you consider custom orthotic therapy. I actually blogged about PF and orthotics both a few days ago. You can read my blog here http://srcpt.blogspot.com