You just have to keep working at it. This includes areas you don’t think are relevant. You are going to have to do all the heavy lifting yourself, but I highly recommend seeing a highly qualified physical therapist. Someone who deals more with sports injuries than occupational therapy/post-surgical type rehabilitations. There is only so much a therapist can do in a once or twice weekly 40 minute or so session. 

I’ve been working on my gimpy right leg for over two years now, including two rounds of physical therapy. MWod is a great resource, but Kelly and gang can’t cover everything. You really need someone who can do a hands-on assessment and keep you pointed in the right direction. Your physical therapist will have exercises for you that Kelly doesn’t demonstrate, including some strengthening exercises. You’ll find that what you learn from MWod will help you understand what your physical therapist is doing, watching what your physical therapist does will help you better understand what Kelly is talking about in his videos. Maybe your back being out of alignment is inhibiting some muscle from firing properly. This was the case with me. My therapist did some manipulations and just like magic I had much improved strength in the glute medius. It was like flipping a switch. There are a lot of possibilities. 
When I first started I couldn’t do the 10-minute squat test to save my life. My foot would turn out and I would fall over backwards just about when my thighs got to parallel. I can now get all the way down and keep my feet parallel. I get just a little big of crackling in my right knee. I used to have major impingement in the front of my ankle, that “bone-on-bone” feeling, along with something going on around the medial maleolus. I find increasing hip mobility also improves hip mobility.