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!

I would recommend changing to a PVC roller vs a foam roller.
Have you had anyone look at your squat mechanics/technique?
It’s always good to have some feedback on your skills. Or video tape yourself squatting so you can see exactly what is happening vs what it feels like.
Address your hip restrictions first you will see the most change.
This may help to rectify the other things you are experiencing.
There are several episodes that hit the things you are asking about. Use the search to to pull the episodes that more closely hit what you are experiencing with each spot. Be more specific to narrow the episodes down.
Squat Quick Test: Is it your Ankles or Hips?
Super Sumo Groin Mob
Episode 363: Pre-Squat Hip Opener Mob-Rx
Episode 269: On the Spot MobRx for Tight Hips
Episode 252: Two Joint Muscles and Your Hips
Episode 239: Hip Extension, Like Pure Melted Gold

Ankles
Case Study: Tight Ankles = Bad Squatting

Knee
Episode 306: Set Up the Knee “Hinge” Joint So That It Will Actually Hinge
Knee Pain? Got Full Knee Power/Range of Motion/Potential–Terminal Knee Extension Part 1
Knee Pain? Got Full Knee Power/Range of Motion/Potential–Terminal Knee Extension Part 2
Knee Pain? Got Full Knee Power/Range of Motion/Potential–Terminal Knee Extension Part 3
Episode 253: Knee Pain Case Study Part 1
Episode 253: Knee Pain Case Study Part 2
Episode 253: Knee Pain Case Study Part 3
Episode 59: Upstream and Downstream (knee-itis). And the Bear
Voodoo Band Your Patella Femoral Pain
Episode 344: Compression Tack and Floss–The Knee
Foot positioning could be an impacting factor. This impacts the amount of torque you are able to harness.
Foot Position Test: Breaking Diane