Mark Rippetoe is a great coach but there are some things I don't agree with. First rule of thumb is if it hurts don't do it. On the other hand, if the knee pain doesn't hurt in a saggital plain, see what happens in a lateral plain. I suspect one of two things, meniscus or patella tendonitis. If you have patella tendonitis chances are your quad isn't firing. One way to check that is to flex your quad like in a leg extension and see if there is a hard contraction, if it isn't chances are that's it.