I had a very similar injury. My running was going extremely well and this came on. In my case, I went to over a dozen good clinicians (ones who worked with pro athletes and taught at top ranked universities), including DPT's, MD's, ATC's, DCs, and DPM's. I went through X-rays, MRI's, orthotics, manual therapy, massage therapy, RICE, NSAIDs, etc. and nothing worked. Nobody could even diagnose me. I went from being around low 30's 10K shape to not being able to run more than about 30 seconds due to sharp stabbing pain. And, like yours it was hard to locate exactly, but seemed to be around the peroneal tendon. Sometimes it seemed to be on the bottom of my foot also.
4 years later of disappointment, frustration, chronic stiffness and pain (with zero training) I randomly found another chiropractor based on a recommendation who did his own form of myofascial therapy. He literally removed my pain in an hour treatment, and then helped me do some neuromuscular training to keep it gone.
I do not believe his training as a chiropractor was what did it, nor do I believe he is the only person in the world who could have cured me, but the point is that it was a long frustrating journey.
Just because a doctor says "tendonitis" does not mean that it is. Is it hot, swollen, and painful (I will leave out the "red" component)? If it meets all three of those things, than it very well may be inflamed and anti-inflammatories are appropriate. However, if it is not hot and swollen, it does not likely have acute inflammation and therefore will not respond to medication designed to treat inflammation.
So, for those reading this who have been through this frustrating type of injury, keep shopping around and find a good manual therapist. If you try two or three and they can't help, don't give up - you will eventually find relief somewhere.