Something came to mind while reading this. Try working your ankles either by getting in a lunge position working it lower and lower if you can without pain. As you get better at it, get it to a high lunge with you back heel on the ground and your back leg as straight as you can. If you can also unweight yourself(lunging between to benches and holding on) you could work the foot in different directions while in the lunge to try and get some mobility.
Another one might be to set your foot up on a box as you would for step ups that would be below parellel. Work your range of motion with your other foot on the ground both front to front and side to side. You will also get the added bonus of some hip flexor at the same time.
Also if you haven't tried deck squats, or squatting while counterbalanced with a 5 or 10kg plate held in front of you. Just some thoughts.