I injured my knee back in 2000, popped it good too. It twisted wrong when I was thrown and hasn't been the same since. For about 4 years after that occasionally it would gimp out on me and reinjure itself.
My ukemi began to suck bad because I was afraid to roll and come up on it with any pressure, my throws began to suck because I was afraid to put pressure on it, and it overall affected my walking and reopened another injury to my left ankle I had gotten about three years prior to my knee going out. Because I was walking so gimply upon my knee my ankle began to swell and ache, sometimes to the point it felt like my entire leg from the knee down was on fire. It hurt so damned bad!
I finally got into a descent training regimen by working it from a sitting position to a kneeling position, to finally a standing position. It still hurts from time to time, and gives me problems, but its rare. Sometimes I feel it trying to go out on me but I reset myself and go again. I try to avoid and adapt around the injury. I too had a mental block from it, and still do to some degree because to be honest, pain is pain, and in a knee joint that can suck bad. I had mobility problems as a result and had trouble completing the simplest things around my house as well as trouble keeping comfortable.
You just have to train through it and make yourself more adaptive to it. Its sometimes a life-long effect, work on it and see a doctor regularly about it. Worked for me.
Good luck to you and congrads on going back to training so soon after an injury.