Thanks Physiobob
What really surprises me is that you are saying that this is common. That makes me feel better, because it'd help me to find a way out of this.
I am actually feeling better now than two months ago. I can bend my knee and often without hearing any clicks in the knee. But I cannnot jog for more than one minute as a am quite unstable. I am biking nearly everyday in the gym for 30 minutes+.
Today I will see another orthopaedist.
I found this article describing a case very similar or same as mine,
Failed regrowth of the harvested semitendinosus tendon: a rare complication of tendon harvest after anterior cruciate ligament reconstruction.