Here is an update- My knees started to get better and then I got greedy and hit some heavy deadlifts and the pain is back. I believe my IT band is tight so I am working on rolling it with a foam roller and a baseball. I am getting a lot of relief. I even tried SLDL's and that aggravated my knees(there again I got greedy and went heavy), I tried to run for a couple of miles and things felt fine until the next day and everything felt real tight.
The good thing is that when I take some time off my knees start to fell better. I hit those SLDL's on Saturday and my knees are already feeling better and its been a few days.
I am going to continue stretching and rolling and I will start lifting in a week or so but I will go way light on the lower body stuff.
Another note-When I was doing all these activities, I never took time to stretch, I am very inflexible
I'm gonna say that it's likely that your tendons are taking a beating and that might be where a lot of this is coming from. If you could I'd really roll with a lacrosse ball, it's a lot safer and easier on you than a baseball. Where is your knee pain by the way?