The less severe knee injuries are usually straight forward and for the most part easy to diagnose (compared to say, shoulders). Take a look at the link below and see if you can narrow the issue down if for no other reason to have an idea of what your dealing with.
In the mean time, considering using small doses of anti-inflammatories (ibuprofen) before and after training. If you haven't already, pick up a pair of knee sleeves, these will help keep the knee warm (can help a lot) or light wraps such as ace bandages if you think its a knee-tracking issue --- I use ace bandages to keep my left knee "inline" and provide a little warmth when pain creeps in from time to time.
Another thing that has helped a lot of people I've come across with knee pain; make sure you staying on your heels during both the descent and ascent. Coming onto the front of the foot puts a lot of pressure on the knees.