Hi Winston. I think you have taken the right turn and as it shows you have less problems with injuries. I used to have a lot of problems with my knees in 2014 and what kept me going again are two things: 1) being grateful for every run you can do with less pain and thanking for that in a sort of mantra (seriously) - thank you for my knees working properly with less or without any pain; 2) doing alternative work outs, like push ups, squats, etc. It really helps to strengthen your muscles and to prevent injuries.
One last advice - I know, that running almost every day is very important for you. You are doing now two days of rest. I have just made the experience that resting for one week really gives you new strength. You don't loose substance and you gain physical and psychological power. You could swim a little bit in that week or doing a 20min workout, but don't run. Maybe it is worth a try. Best Frank from Hamburg