Thanks everyone, you always have great advice. Yeah... *sigh*... I know now that running for 40 minutes was too much. But I have lungs like a horse and can ride a bike for hours, so of course I was going to go out and do a "real run"... 
I'm such an idiot sometimes. On a good note, I went climbing yesterday, my knee hurt a little bit climbing but is better today. I'll go check out some exercises.
Winter riding is much less about badassery and much more about bundle-uppery. - malkin
1995 Kona Cinder Cone commuterFrankenbike/Selle Italia SLR Lady Gel Flow
2008 white Nakamura Summit Custom mtb/Terry Falcon X
2000 Schwinn Fastback Comp road bike/Specialized Jett