Even on the days you are running, you might consider dropping the weights on the squats a lot, or only doing bodyweight squats, until you have the form nailed.

I suppose you mean 'not'? I guess I'll see how my knee feels in two days. I've never had problems with them before and I ran yesterday, so it might also be from that and they just need a day to recover. I can't really pinpoint whether it's joint or muscle pain, which leads me to believe it might be muscle soreness. I have arthritis, I know joint pain ;)

Thanks for the links. I think I already read half of them, but not the others. I find things a bit hard to find on Stumptuous.com.