@Sagetek If you look earlier in this thread, my Dec 9th, 12th, and 19th posts correspond to 11/12 weeks. I was just starting to do indoor rock climbing. It was scary and a bit painful, but I was soooo excited to be back to what I loved and things seemed very promising for the future. My climbing has been a bit better and less painful every single week since then (I climb twice a week).
I stopped the "tough" PT around 8 weeks, after having a couple setbacks. My flex wasn't great back then, because I was always a bit swollen from the PT. We hardly worked on flex actually, because it was adequate in the eyes of the PT. Back then, we were working more on re-establishing neurological pathways, coordination and balance. I like really hard challenges, and it was very hard. I took a couple weeks off, and then switched to a PT that I've used on and off for years (for other problems). I continued seeing him until last week. He had a different approach, and it was at his office that I started making good gains on flex. I think that pic above is about 140º.
As for "mystery pains" : at 11 weeks, the inside (medial part) of my knee really hurt if I pushed the inside of my foot against something. Scuffing dirt back into a gopher hole hurt. Frog kick swimming (like when you do breast stroke) hurt. etc. That was just a very sore medial collateral ligament. It got better.
At your stage, expect to have various pains come and go. Actually, I remember having tibia pain back then. It felt like bone pain, and I figured it was from driving that huge anchor into the marrow. It went away, but I still get the bone ache once in a while. It reminded me of pains I had during growth spurts as a kid.
I have one long lasting mystery pain. It hurts in the center of the main joint, which seems weird. It happens when I try to support my leg in the air sideways, and then flex and extend the knee joint. Like a side karate kick. My present PT doesn't have a clue, and neither do I. But I carefully/gently go through those motions every day, and it is improving.
I love CO! What part do you live in? I've done about 20 of the fourteeners, mostly the more technical ones. A few, like Longs in mid-winter (north face cable route) were mini-expeditions. I mostly go to the San Juans, because they are close.