OP, I had a complete tear of my right PCL last summer (2010). Took me a few months to get back into lifting and running, I was actually well ahead of schedule. Anyhow, I developed severe tendonitis of my right patellar tendon due to the injury (the PCL never reattached) and overcompesating. I took the time to even out my imbalances. My right hip down to hamstring had become weaker and was causing the pain. I addressed this issue with posterior chain exercises and hip mobility as well as got a patellar knee strap for days I run or push the prowler.
Also, I was letting my knees travel too far forward during the last part of my squat. This was also causing some of the pain. This was pointed out to me by Juli who works at WFAC (Rip's Gym in Tx). So, your knee issues may be due to an imbalance, improper running form, bad squat technique or a combination.
Wendler also recommends weighted walks or strongman type conditiong. If you're trying to gain weight, doing barbell complexes may be counter productive to your goals. Increasing conditioning (or GPP) AND trying to put on size at the same time probably isn't the best combination of goals. How much do you weigh and how much size are you trying to add?