I feel none of this happened till I became addicted to BOSU-BALL squats (which wreak mechanical havoc on the ankle joint in all directions)
That's the truth.
whether you've done damage or whether the problem is related to the bosu ball is not something we can tell over the interweb.
Step 1: stop doing bosu ball squats.
Step 2: if there is pain go get checked out by a health care professional and follow their advice instead of the steps I'm suggesting below.
Step 3: Stretch and foam roll areas that feel tight. work on foot and ankle mobility. work on single leg balance exercises in socks or barefoot (not on a bosu).
Step 4: switch out your ball of foot squats for split squats or single leg squats for awhile (2-4 weeks)
Step 4: try the squats again and see if there's improvement in the form.
Going for some massage would also be a good idea. And if you can't get perfect form with your squat, consider ditching them altogether. It is a good exercise for the right person, but bad for the wrong person. You don't need them to get strong and powerful.