The biggest cause for peroneal tendonitis is over pronation of the foot.
Barefoot running often helps with this so consequently made the pain disappear.
Unfortunately you have made adaptation to the tissue previously. which you are now suffering from.

The numb toe was no dout tarsal tunnel syndrome and is a sign things are very now chronic.

The tight calf is also a sign of secondary compensation.

These changes along with the amount of torsion you are now puting through your knee due to change in squatting form is scary.

If you like training go see a physio therapist or shock wave therapist and get a pair of decent orthotics at the very least.
Bite the bullet and see someone or risk heavy disabling injury developing.

In the mean time ice and rest will help.

Good luck

Dr. Niall Marshall-Manifold
www.londonfootpainclinic.co.uk