First, I have no qualifications, just a random voice on the internet. So, of course your best advice would be to consult with an experienced professional.
With that disclaimer, I would urge you to look at the work of Keith Baar on connective tissue. He has published a lot of research on tendons (assuming your issue is the quadriceps tendon) and advises many elite athletes in many professional sports.
I am in the middle of starting to test some of his ideas on myself but I have not implemented all of his suggestions yet.
He has advice for restoring healthy connective tissue, as well as how to periodize training for those who are already healthy.
In a nutshell, in a case like yours, his regimen would probably be something like:
Take 15 mg of collagen or gelatin with 50 mg of vitamin C.
About 1 hour later do 30-second isometric squats reps. After a rest, do another rep until a total of 5-6 minutes have passed.
Repeat this (including the supplements) one or two more times in the day, with at least six hours break between the isometric sessions.
If you are still doing your endurance workout, take the supplements an hour or so before that workout and then do the isometric workout at least six hours before or after.
You are relatively young. Have you had non-contact sport injuries in the past? If so, did they tend to be muscle tears or bone, cartilage, tendon, or ligament problems. Depending on which type, the answer would suggest what kind of training to program once you have healed.