My knees used to kill me after running 10ks (I never made it to half-marathons!), but then I started taking omega-3 fish oil and it has made a HUGE difference in my knees. They rarely hurt anymore. You may want to try that along with your exercises.

sorry that your knees are hurting so badly. I've been reading more and more on knee issues coming from higher up. My knees also hurt when I run (especially downhill). I've started training my core while doing leg workouts.

G'day MMA... I used to have alot of trouble with my ankles and knees, when I first started weightlifting because of the extra weight. To strengthen your ankles you can do simple calf raises with extra weight.
As for knees, just strengthen your quads and hammies. Be careful when doing squats though, ATG can put a lot of strain on your knees and have the reverse effect of what you desire.

Good luck!