For the most part, rest is your best bet. Also, while I am currently a medical student, I am not a board certified physician, so I recommend a trip to see your doctor. If you've stopped running for the most part and still having issues, time to talk to the pro as there may be structural issues at play.
As to the barefoot issue, I only run barefoot on the beach for the same reasons you seem to want to continue that way. My knee, which was the reason I left the Fleet in the first place, has been operated on more than I care to remember. It is a source of chronic pain, even when I'm not running. Barefoot on the beach is heaven for me. When I'm not in the sand, I've got a pair of those Reebok ReeFlex shoes and they are amazing. Love them as they are lightweight, and free moving. Won't be running in anything but them for the time being.
Hope this all helps.
H
"Those who expect to reap the blessings of freedom must, like men, undergo the fatigue of supporting it."-Thomas Paine
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