Post arthroscopy problems, bone misalignment

Hi all.

Currently, I'm a 21 yr old male and in May 2017 I had right knee surgery for a torn lateral meniscus and cyst removal. The tear was really bad; I had an enlarged meniscus and the tear was regular through that portion and then horizontal through the outer portion of my meniscus. Where it met the joint capsule, a cyst formed at the joint line just posterior to where the IT band comes down past the joint. The surgery removed the extra meniscus, "repaired" the torn portion using a blood clot thing they made, and the cyst was removed.

Fast forward past months of both physical rehab with a PT and personally, I was still struggling with the scar tissue left behind by the removed cyst and nobody could really give a straight answer as to how to deal with it and what not other than keep strengthening the joint and leg muscles. I returned to sports such as basketball and running on and off and although I was cautious with impact and such, I still experienced trouble with my joint strength and inflammation in the general area of my repaired meniscus and the scar tissue from the removed cyst. After almost 2 years of assuming that all my problems are just due to that scar tissue and the need for better rehab regiment, I fear that this may not be the actual problem. After doing a lot of research over time and obviously inspecting my own knee hundreds of times over the past year+, I am confident in saying that I think the bones in my knee are slightly misaligned. The area where the cyst was removed has felt very hard and has kinda stuck out a bit since the surgery. I was told its just dense scar tissue and it will mostly go down eventually. After almost 2 years I think that is wrong and that actually what I feel and see is the edge of the top of my tibia. I feel this is true because when I look at the medial side of the same knee, I see that my femur sticks out a tad bit more than the tibia does, in relation to the medial side of my healthy knee. I went to my doctor with this information(who by the way originally thought that the bump was my fibular head, haha lol) and after convincing her otherwise she said that it may be a good thing because it isn't too much of a difference and it reduces friction on my IT band. I understand this but I'm still worried because this misalignment is only true when my leg is straightened. As I bend my knee, I feel and see the joint line realign, but as I straighten it out and the knee is only like 10 degrees bent, I feel a small pop and see the edge of my tibia stick out just a few millimeters where that scar tissue is.

My other concern is that any actual scar tissue that is over there is somewhat wrapped around my LCL because I can't seem to feel out the whole ligament as thoroughly as I can with the LCL of my left knee when I'm sitting in the butterfly position. Additionally to all this, a recent MRI revealed I have a sprained ACL. My doctor only knows this from the radiology report but she did not review the actual MRI disc herself. She didn't exactly tell me what to do about that because we both understand that those can heal on their own but she wouldn't say that if it meant her losing out on another potential surgery to perform and get paid for. After about 3 months of straight rehab and no strenuous sports, my ACL has not healed. I know this because I feel the pain when I descend downstairs and put all my weight on my right leg as it bends and I step down with the other leg.

In short, I have a sprained ACL to an unknown degree, I fear the strength of my LCL is compromised due to scar tissue from the removed cyst(nothing about this on the MRI report), and I fear the slight misalignment of my knee when fully extended is a problem that may have resulted from the compromised LCL and may have contributed to the sprained ACL. What can anyone make of this and, what should I do?

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