This sounds like a meniscus issue, which heals slowly, if at all. Popping and swelling are rather classic symptoms of that.
- Squatting ATG is not recommended because you must relax to get there, especially with low bar squats. Are you low bar squatting? If so, start doing it correctly. If not, it is time to get with the winning team.
- Yep. Once again, you should learn to squat correctly. Crashing into the bottom of the squat is not a good idea.
- I would wrap if I were you, provided you don't have a more serious meniscus issue that requires a surgical fix. It would be wise to get a diagnosis. In the meantime, wrapping or wearing knee sleeves to provide some support should be on your list of things to do after fixing your squat and figuring out what is wrong.
- Unlikely. Some people have hypothesized that this happens with anabolics, but I think it is unlikely in your case. You are more likely to have a partial meniscus tear.
- For you, warming up more probably is a good idea.