Good timing with this topic.
I've been struggling with a clicky right knee for about 4 months now. 2 months ago it turned into a dull pain. Click occurs about midway between standing and a full squat. I saw two different ortho Dr's who diagnosed patellar mal-tracking and patellofemoral pain syndrome.
Continued squatting 3x per week, while doing PT. Pain escalated.
Started seeing a chiropractor 1x per week with new PT as well, got slightly better, but continued squatting.
Now, I'm at the point to where I have to take time off squatting. I'm about 10 days into no leg work. Knee feels drastically better, but is still loud. Climbing stairs I get that predictable click and kind of grindy noise.
Had X-rays done which did not show any abnormalities. Neither Dr's nor Chiro says there's a need for an MRI.
I'm working on trying to re-establish proper tracking through mobility, stretching and strength training...focusing on hips, glutes, etc.
Also, as you have, I have straightened up my foot orientation on squats. I find it helps me keep everything aligned and neutral. When you get so f'ed up, it's almost like you have to go back to the basics and relearn proper techniques and remove the hacks.
Knees are so important. Take care of them! Take time off before forced.