So the finally results after months of rehabilitation –  In bullet form so its not such a wall of text
–    I have been running for 4 months now and did my first 10km last weekend without any trouble
–    I am squatting heavy, jumping, burpee’ing and everything else without pain
–    The peroneal pain is mostly gone, though does occasionally flare up if I push myself to hard or over stretch the area
–    The peroneal still clicks, but I have decided its something I will just need to live with
My rehabilitation plan was sort of all over the place, but the most important things I did –
–    Minimizing stretching and massaging of the peroneals. Poor guys were beat up and did not need it in my case. They needed strength.
–    Doing 50 inversion and 50 eversion banded ankle on both legs every day (I can actually see the development of the peroneal muscles)
–    Doing lots of hamstring strengthen, active stretching, etc (think Romanian Deadlifts, reverse lunges, etc)
–    Glutes, glutes, glutes, glutes. Every day. Several times a day. Because you’re a PT you should know which ones to do. I am still working on these to get my glutes working correctly again (Bonus, my butt looks great now)
Not sure if this helps you much, but for me the biggest help was making things stronger, not ignoring them. I clearly over complicated the issue, similar to what I did with my shoulder issue which I talk about in a different thread (now 100% fixed), seeing a much more serious problem that wasn’t actually there.
I won’t be racing this summer, but my goal is to race next year in a half marathons which no longer seems a pipe dream.