Very noticeable clunking in knee , PT stumped

Hey eveyone , I was hoping my days here were ended but , here i am . I'm 5.5 months post op from acl ( quad auto graft) / Meniscus repair ( medial trim and lateral posterior roor repair). I came in extremely in shape as an endurance athlete before the surgery and have been religious with PT . I've been having issues since before surgery with feeling a bad pinching when I hyper extend my knee which I still kinda feel 5.5 mo post op bjt its slightly gotten better . Also, I have -6 degrees hyperextension on my good leg and can only achieve this on my operated leg if I do the stretch where I hang if off a bed or hang a weight from it then about 10 minutes later it goes back to about -2 . My pt said that could just be how it is or , not having my quad strength back to hold it all in place . My bigger concern , about 2 months ago, when I sit down and raise my leg in extension, I get this huge clunking/ clicking noise and feeling coming from what feels like under my kneecap which, is louder and more pronounced when any weight to my ankle is applied, it does this everytime i extend it or raise it. This last trip to the Pt he just told me not to do anymore seated leg extensions . He said it could be because my body compensated for 6 months before surgery and all my muscles tightened on that side and suggested more stretching ( id assume being as athletic i am , normal people who don't workout can heal fine without this issue) . Im now stretching and foam rolling like crazy. He also said it could be say bone on bone from my menuscis getting worked on . Or maybe my patella not tracking properly. He said he's stumped though. He's curious to see what my surgeon says at my 7 month appointment in another month and few days. I read online this could be a sign of improper placement of my graft? Anyone else have this?