To start off I am not a doctor... I went through something similar to what you are describing a little over a year ago. I was having sever pain on my heels and was diagnosed with Plantar Fasciitis. Typical treatment was ice and stretching which helped but did not make the pain go away. What I found is plantar fasciitis is common in people who are in their mid to late 40's and over weight. As we age and gain weight the arch drops and stretches the tendon where it connects to the bottom of the heel causing micro fractures. I tried ice, stretching and message. What worked for me was getting good quality shoes with high arches (Finn Comfort shoes) and avoided going bare foot. After about 8 months to a year I am pretty much pain free but still wear the good quality shoes.
During the period of trying to figure out what caused the pain I was convinced the pain was from riding as my foot would hurt about an hour after riding. My own solution was going with high arch support shoes and continue to stretch. Today I am good but when I spend a weekend hiking or doing things in tennis shoes my feet let me know that its still there.
Anyway, I suggest following through with he doctor and see what they say. If they suggest shoe inserts and insurance will cover it you should try that. No matter what the recommendation is, it will take time for the pain to subside.
I went to the 'Good Feet Store' and they tried to sell me $300 + worth of orthodics. I then went to a local high quality shoe store and ended up buying the Finn Comfort shoes and sandals which has resolved my problem.
Good luck... and don't try to tough your way through it... it only gets worse.
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Uphill or downhill; headwind or tailwind; Pavement or Dirt ... it's all good.