This doesn't really seem like anything out of the ordinary. You say you walked on your toes for a long time so now that yo have a change to have a heal-toe gait all sorts of foot pains will present due to soft tissue contractures being stretched out over time. On intermediate remedy will be to wear running shoe style trainers with a high heal, or even healed shoes until you ankle regains its full dorsiflexion (bend).
You physio should be able to test the scenario of the knee being involved by looking a the amount of bend your ankle has with different amounts of knee flexion. Perhaps by sitting you on the plinth and looking at the heals ability to sit flat with varying heights of the bed. You might simply have a tight soleus (part of the calf muscle) and so the deeper you knee flexes in sitting the more then ankle is forced to flex to compensate. Again restriction here is normal from what your history says.
As for the posterolateral instability, well that's perhaps par for the course. This is likely to be the ACL injury but you are noticing it now as you have regained full rotation. One might like confirmation that the graft is in place.
Overall it sounds like to are panicking prematurely and perhaps because your therapist has not fully investigated the situation with you and explained what's going on. Also a graded return to flat shows would be recommended with more or a healed shoe in the early months. Also get some deep tissue work done on the deep calf and peroneal muscles on that side plus some firm through range of motion ankle joint mobilisations.
Good luck