Your message calls only for one answer: Squat DAILY according to the Starr rehab protocol! Also do do your PT exercises daily. By now you should know how to perform them yourselves. Of course, I don't know what your PT has taught you. Without that knowledge I can only advice you to not be doing any stretching exercises; but to focus on the strengthening PT exercises and to progress the resistance used in these.
Pain is just the way of your body telling you that something is amiss. But you know what the reasons for your pain are. You also know what to do about it. So DO IT and don't stress out over not being 100% healthy. Looking for excuses not doing what is necessary, won't get you any better.