Well, I know for me... when I was in full on training mode for my HIM.. on some of my long distance runs I would get knee pain.
Although, it was not consistent knee pain. Just sporadic. I had a time period of about 2-3 weeks where on my long runs I had some serious pain in my knees. It woud be tender to the touch even.
Then, it just went away. Poof! It was gone. No more knee pain. It was really weird.
As for your stride being changed, that might cause pain. I would suggest you getting a video camera and recording yourself running fast and then slow. Maybe you can see what you might be doing differently. I know when I had pain when I ran, I would pay attention to my form, make a minor adjustment and it would help.
"Life is not a journey to the grave with the intention of arriving safely in a pretty and well preserved body, but rather, to skid in broadside thoroughly used-up, totally worn out, and loudly proclaiming: WOW WHAT A RIDE!!!!"