Metatarsalgia (Capsulitis) on the 5th metarsal...

...anyone ever had this?  I was diagnosed with this last week after 3 months or so of trying to figure out what was going on.  I should have seen a doctor earlier.  I really thought I had a stress fracture in my 5th metatarsal, but x-rays came back negative.  I was actually told I have healthy feet bones and that this may be a result of over doing it (ran two road marathons, two trail marathons, a trail 50K, and one trail half between October 2011 - March 2012).   I assume more stress was placed on my feet when I started trail running late last year.  I have not done any activity going on 4 weeks now and the soreness comes and goes.  He put some padding on the inside of my shoe to alleviate pressure on the pinky toe joint.  It has helped.  He has suggested orthotics because my other issue is I have flat feet and overpronate.  Anyone been through this and do you have any suggestions for quickly getting back to running?  Thanks!