Superman Beyond, maybe your case is similar to mine. I always practice pistols barefoot and often run in minimalist shoes. This exposes my main flaw: right ankle instability. Sometimes I have to wear orthotics to relieve the pain in my achilles tendon-in fact, I normally use them in winter when I am not training, and, if necessary, when I go running too. My orthotics have been prescribed by a doctor who, on the other hand, favours my barefoot practice provided I use my common sense and stop when in pain.
You should see a doctor. At least if, after a rest, the pain doesn't subside. Meanwhile, stretching and ice can't do any harm.
It seems you have already the pistol skill. If you can do eight with each leg, your nervous system has learned the movement. In a way, you nervous system "owns" it. At this stage, shifting to Goblet Squats, FSquats, Zercher Squats or Cossack Squats may even help you with Pistols. Another good option would be Face the Wall Squats. I noticed improvement in pistols after a short period of Goblet Squats.
Try also to hold the bottom position of the pistol for time after negatives. If your case is like mine, it is the positive upward portion of the movement what triggers the pain. Negatives and bottom isometric holds help me. Try it. It might work.
