RC, sorry to hear about the injury and surgery and sorry you are having pain. Most of us with RPT have the same issues with steps, as I am about 8 months post surgery and going down is a chore I try to avoid. I am not sure how the recovery and healing were for a partial tear, but I was immobilized for the first 8 weeks in braces as I had ruptured both tendons. I have read some posts about misalignment, but nothing on correcting it. I spent a lot time massaging my kneecap, tendons and knee area to break up the scar tissue in hopes of avoiding some of the perils others faced in their recovery. But, I have lots of grinding, sometimes you can even hear it, but I had not heard about getting the knee joint lubricated. Check out the board and you will find some good info. Lots of people hear all with different situations and lots of good advice. Ask your OS and PT for advice and then double check it.
TOM