I'm another one in the barefoot as often as possible camp. I had a disaster with my leg which I later discovered could have been prevented if my GP had paid more mind to my PF. Mine was basically a symptom of a really tight achilles tendon. Legs are brilliant things, but you need to keep all their components stretched and looked after nicely or things tend to have a domino effect - I carried on walking with 'shin-splints' and ended up popping my hamstring, tearing the cartilage in my knee and after an MRI they discovered I'd been walking on a fractured tibia (which had been put under stress by my tight achilles!), and all the other damage had been caused by a sub-conscious over-compensation from other areas of my leg and back to try and minimise the pain.
Physio recommended going barefoot as much as possible; stretching every part of your legs out regularly even if you don't think you've particularly used them and flexing your feet as much as you can stand; and I found the insoles for your shoes really, really good, particularly in walking boots. Check to see what your arches are like - I have really high arches and you can buy trainers / fell-runners that have extra support for high, and low arches that will help (I wear Brooks and I find them brilliant). I was warned dead against wearing anything with no support, like Converse that are completely flat on the sole, even for short periods of time (for example, the walk to school).
Some people swear by things that are very hot or very cold (everyone is different) applied straight to the underside of your foot to relax the area, but it didn't really work for me.
Hope it gets better soon!