Sounds like a Patella Femoral Pain Syndrome or something similar.
Long story short, your knees have certain degree of stress they can handle and adapt to. To make your knees adapt to more stress, you can only add a stress that don’t injure your knees. If you exceed your knees envelope of function, your knees get inflamed. And if you keep exercising with this inflammation, you injure your knees.
The most important thing you can do is get back to exercising with loads that your knees can handle. If you can’t do a full weight body squat without pain, then use a wall or something to do 3x8 assisted squats. Increase the load extremely gradually. What you essentially did was allowed your knees to produce inflammation and pain and then you COMPLETELY cut off exercise. Now, the envelope of function of your knees is absolute shit. You have to work within that shitty envelope of function.
I’m dealing with something simimar myself, m8. If i’m not making this clear, ask me. Or read this paper (it lays out more clearly what i’m trying to convey):
http://prdupl02.ynet.co.il/ForumFiles_2/19447772.pdf
Also, this article by Rippetoe himself hits the nail on the head how an injured athlete needs to approach an injury:
https://startingstrength.com/article/rehabilitation
Good luck nigger