Tri Girl... I second knotted's suggestion of having a PT check for other imbalances. It sounds like you have not stopped running through this. Perhaps you do need to give your feet a break to recover.

I had a bad case of PF about 6-7 years ago, so bad I could not walk for a block without major pain (forget about running). This led me to buy my first bike as an adult! I did stop running for about a year and a half --a total bummer. The pain subsided gradually (night splints, stretching, PT, massage, iontophoresis, taping, icing, pills, you name it). I used over the counter inserts and Birkenstocks. Once the pain went down to just noticeable after walking, I slowly started "running" again: started with 15 min walking, 5 min running, walk back home, stretch/massage like crazy... The pain eventually disappeared, but I'm still mindful of the shoes I wear. And I run pain free or, at least, free of PF pain.