Hi
I wonder how much of your rehab was hamstring focused initially and did it involve any eccentric hamstring work?? Plyometrics and very intensive and if you started them with a hamstring that wasn't completely rehabilitated, it is very easy to cause an injury. It sounds to me like you've pulled your hamstring and have secondary patellofemoral symptoms due to not having treatment on it and have been wandering around with a stiff knee.
My advice is to get some treatment focusing on your hamstring and patellofemoral joint (kneecap) Your patellofemoral joint commonaly refers pain to the medial aspect of your knee.
You'll need to get massage on your hamstring and work on stretching and strengthening (especially eccentrically) If this all sounds a bit foreign, then flick me an email as I may be able to send some examples of exercises. They'll need to be done under the supervision of a physio however..
As for how your semimembranosis tendon is meant to look and feel....it is natural to have some scar tissue and wasting. This doesn't necessarily need to affect the function of your tendon if you've had the appropriate rehab.
Hope this helps
Rachael.