I hear ya man. My case is about 90% similar to yours.

Have you tried single leg extensions with a weight for squeezing out 5 reps? I’ve been doing these all along and they’ve done a few things for me.

1 – They have helped repair the patella tendon, I feel in a similar way that eccentric decline squats help to rehab the tendon. By stretching and pulling at it to increase blood flow and break down scar tissue.
2 – They have helped get the timing, in particular of the VMO, of all 4 quads to fire in unison and keep the tibia rotating around the knee joint in proper alignment. It’s actually pretty interesting, because sometimes having an injured tendon can provide direct feedback – when I time all 4 quads right, my tendon won’t feel pain, but the moment my VMO fires late, or my upper quads aren’t really engaging because maybe I’ve dropped my posture from the glutes up, my tendon lights right up with pain to tell me something is wrong.

When you do them:
    -Sit with proper posture in the upper body and tight glutes.
    -Don’t point your toe, pull it back as far as possible.
    -Make sure you’re still using the principles and torque through external rotation.
            You should feel that you have to rotate your leg a bit and put some tension at your knee to get your quads to really pull in good balance on your patella.
    -Lastly, (I’d like to know what happens to you) focus on really using all the muscles around your knee. When I do this, it really kicks my VMO in earlier than it normally would, and I can feel that side of the patella pull in unison with the outside part of the patella. Also, I almost always feel and hear the inside (VMO) part of the patella crack and kind of tear for the first few reps. Sometimes I can get this same crack and tear to happen if I just block the upper part of my foot on something heavy and flex my quad hard in a gradual manner. After a few reps of the tearing and stretching of the actual tendon, the rest are nice and smooth.

I really don’t like the idea of isolation training – but for the purposes of correcting muscular imbalances, I think they can be well utilized. Once the balance is achieved, I would think the training would shift to jump boxes which still focus on a stable spine and upper body, with the power coming from the legs, and the intensities can now vary from a single weight, to an environment of higher variables. Then also start an overall strengthening program that involves various compound lifts and keep the isolation work to a minimum.