Your injury is simple to diagnos, it's obviously brain damage.
Seriously, I think your injury existed prior to your stretching. It sounds like a biomechanical problem, likely caused by wearing the wrong or too worn shoes. It simple terms... runners knee.
When your feet don't land properly the rest of your leg must stabilize it. That is why some runners will have a problem with their ankles first, then their knee, then their hips... think of your leg as a pendulum. It doesn't take alot of movement at the base of the pendulum to cause a significant swing. Read chapter 14 of the "Lore of Running", or you can probably find more in depth info at webmd.com.
I think your "stretching" just aggravated an existing problem.
Or the other possibility, somebody is sticking needles in a voodoo doll.