Sounds like you have chronic inflammation / tendonitis or strain. Yes, see your physician, and use rest, ice to help reduce the pain and swelling. You are also correct that there is a biomechanical issue, likely to do with the lack of proper flexion in the arch of your foot. You'll need to see an orthopedics specialist, as you will probably need orthotics correction for your feet. As well, you need to have your athletic shoes looked at; chances are they are improperly fitted or worn. Improper or worn shoes will cause biomechanical issues in stride, and that can cause a chain of injuries between the foot and hip/lower back.
Your doctor or PT will provide you with exercises to strengthen the tendon, once the damage has been assessed, injury reduced and you've been given the OK to for strengthening physical therapy.
P-funk may elect to answer you question on exercises. At this point, before you have seen a physician, I'm hesitant to recommend strengthening exercises.


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