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Poor glute activation can cause lack of external rotation because the glutes are external stabilizers to a degree. This leads to valgus knee(knee collapses inward) which means your feet might be pointed outward and your knee is also not tracking properly over your ankles. I would hit your quads, keep hitting your TFL(mine definitely gets tight), work on your glute activation, use a lacrosse ball on your glutes, hit up your IT band, stretch the hell out of your hip flexors (couch stretch) and when you say 12g of fish oil how much combined EPA/DHA are you getting? 1-3 grams is optimal so 3g for your bodyweight would also be optimal. It should say on the bottle.
If air squats are bothering your knee then take it easy! Weighted squats will surely add to your dilemma and overhead squats require a high degree of mobility so only do stuff you are comfortable with and work your way up. My overhead squats in particular are limited by my extremely tight upper back/thoracic spine and lack of external rotation in my shoulders. So to recap:
Work on quads, hip flexors, glutes, glute activation and any area upstream and downstream.
A knee problem can be caused by the hip or ankles and vice versa for all those systems. If you have any other questions I will do my best to help you out!