Hi Sam, just read your post. MCL's are painful and they remain painful for a long time. It was funny but reading it I was thinking all this guys needs is some frictions to the ligament and low and behold that was a treatment that worked. From you recent observations the knee gets into trouble when sitting for long periods. This is in around the 90 degree flexion mark which is also specific to the medialmeniscus at that range. The ligament itself communicated with the meniscus and different fibers of the MCL are under different amounts of tension depending on the position of the knee. This is a way that the brain helps us to understand joint position without having to look at where our limbs are all the time. Anyway the point being that the position of the knee is different in sitting to that when walking.
Yes I agree with pronation contributing to issues here but you were OK prior to your injury so let's not over analyze that. Orthotics are always useful in part. Connective tissue, especially degenerate tissue, does not like being help in the one place for a long period of time. Doing so leads to pain e.g. bend the finger back and hold it for a few seconds and it doesn't hurt. Hold it there for 5-10mins and it become really painful. I would get someone to assess the medial joint line to see if in fact the meniscus is irritated and if so it can be frictioned as well. They I would friction the MCL in the position in which you get the pain.
It's unlikely you'll need an op as I see dozens of presentations like yours every year and less than 1% need investigative surgery. Best of luck