I'm afraid this is a really tricky one for a layperson to help you with. It really depends how severe the rotational abnormality is, and only the surgeon can judge this.
If the pain is primarily down to PFS or patella tendon issues, PT is by far your best bet - but you need to find someone who really understands these issues. I know from personal experience how debilitating PFS can be, and I do know that a lot of the pain and symptoms you describe match severe PFS very closely.
I went through years of pointless physio in the UK with therapists who didn't really understand the problem. PFS is a symptom - to fix it, you need to deal with the cause (in my case, maltracking kneecaps due to a combination of overpronation and very tight IT bands and quads.) My UK PTs focused on the symptoms, and never even mentioned what could be causing them. Consequently, nothing worked.
When I started working with my current PT in Canada, he took a huge step back and rebuilt the way I handled my knees. He dialed back all the exercise exponentially for a full month to allow the inflammation to settle, got me in orthotics to address the overpronation, used regular IMS to release all the tight muscles, and then very gradually built my exercise program up again to gain strength in the right areas while not overstressing others. The results were dramatic. I went from not being able to walk down stairs or run at all to comfortably running down stairs.
If the rotational abnormality is severe enough, nothing short of surgery to correct the rotation is going to help. I'm not a professional, but my suspicion is that this is not the case for you - you wouldn't have been able to run the distances you were doing previously as consistently if it were. Of course, you may have suffered a soft tissue or bony injury from the fall that is throwing a spanner in the works, and this is definitely worth more investigation. But overall, finding a PT who really understands PFS issues and what causes them is probably a very good option at this point, given the likelihood of this being the source of your pain.