A few questions and comments below:
1. What hurts it exactly? You mentioned that squatting with toes and knees out, there is no pain, but you didn't say what stance hurts your knees? Only with back squatting? All squat motions? Lunging? Stairs? high bar oly squats? What is your normal stance?
2. 1-2 grams/daily of EPA/DHA is more like a normal dosing, I would recommend doubling or tripling that amount for a short amount of time when you have a lot of inflammation.
3. I would say take it slow as you need to, I once had a nagging elbow tendinosis thing and when I finally felt like my elow was ~95% again I hurt myself again! The 2nd time around I just completely avoided movements that hurt it and took my rehab seriously. Go fast heal slow, go slow heal fast.
4. Foam rolling and stretching is all well and good but unless you can figure out what is the cause, what I mean by that is say one day you find a puddle in your kitchen, so you mop it up, you find a puddle everyday for the next few weeks. You mop it up consistently but it's always back, so intuitively there is something else wrong right? There is a leak going on somewhere that needs to be fixed. For now you need to find the root cause of your knee pain, so look upstream and downstream of your knee pain
Check out these videos below for some food for thought:
A great comprehensive article by Steven Low: