I know it's tough to explain exactly where the location of the pain is on the forums, but is the pain on the outside of the knees on the back or closer to the patella (knee cap)? I had all kinds of pain and microtears on the back of both my knees. An MRI and x-rays was taken on my left knee because it was the most injured out of both of them. I went to physical therapy for the injury and what they had me do works like charm: specific stretching and foam rolling.

Now, here's the key: low intensity stretching for long periods of time- none of the intense stretching in quick bursts nonsense! Also, make sure that you do the stretches after your muscles are somewhat warmed up or you'll risk causing more micro-tearing. So, if you don't ride one day, stretch at lunchtime of after work once your muscles have been working a bit. I followed this regiment and was back on my bike about 90% pain-free in a week. It's all about **myofacial release** (where the foam roller comes in). Google myofascial release. If your facia is tight, it will pull on different muscle groups in a bad way. So, if your fascia is tight in your quads, you'll get injuries in other arts of the body, like the lower back, hamstrings, et al.

They taught me all kinds of relaxed positions where I could read a book, play chess with friends and relax while getting my stretch on and it has to be done DAILY! Even if you don't ride everyday, stretching has to be done everyday. I concentrate on my hamstrings mainly because this is where my injuries were the worst. Foam rolling once in a while, but the **low intensity stretching for long periods of time** is the cure.
Maybe one day I'll get to scanning the handouts (about 20 pages) of all the stretch positions since this is a common question on the forum. I'm not sure if I'd get in trouble by the physical therapy business though! PM me if you are interested and maybe I can get them to you- THEY WORK! Good luck and I hope you heal up quickly, I know what it feels like and it sucks.