Progression for Quadriceps with Tibial Tuberosity Pain

Hello Everyone

Brief intro:
For 16 months now I'm unable to perform any sport activity due to pain in my left tibial tuberosity. I'm 30 now and I had Osgood-Schlatter when I was 11 or 12 y.o.
The doctors haven't yet gave me a clear and sound diagnosis, but it's quite obvious that the pain is in the distal insertion of my pattelar tendon. I've tried physiotherapy for two months last year but it didn't help me at all, in fact I felt much worse during that time. Now I'm once again trying to perform some exercises the physio prescribed me, but paying better attention to what actually helps me and what doesn't.

The Problem:
It seems a concenssus among profetionals that eccecentric squats on a slant-board and quad stretches are 'musts' for treating many sorts of pattelar tendinopathies. The problem is that if I do ANY knee-flexion exercise or stretch the quads for more than 15 seconds I'll have pain for the next 1-2 weeks. During the exercise/stretch I don't actualy feel pain, just a slight discomfort at most. After a few minutes though, it starts, never too hard but persistent.

The Question:
Given the problem above, I've been doing only straight-leg raises for my quads for the last two weeks. I almost don't feel pain anymore (as long as I don't try any knee-flexion exercise) but I know it just won't cut it. So, what kind of progression would you guys recommend to me so I can start stretching my quads and doing some knee-flexion (and hopefully squating) again?