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Alpha919 and Lance,
I used to deal with the same thing. Anytime I would squat or lunge/ any leg movement my quad tendon was ON FIRE. It was so bad that it felt like it was going to rip right off at some points. The things that helped me were what you are doing, but what helped the most was getting my hip flexors loose. The couch stretch was numero uno for me but also taking that LAX ball from your patella all the way up your quad to your flexors, tack and stretch all the way. The last thing was dialing legwork back for a week or so and doing the mobility work for 30 min a day for that time. It worked for me,maybe it will work for you!
Hope it helps