I have the shimano SPD 505's - with tension set very loose. I have two, maybe three thoughts on your knee/leg pain:

1. when clipped in, different leg muscles are used depending on where you are sitting on the seat. i.e. front of seat/back of seat. I'm wondering if changing the position of the seat alleviates this pain for you?
2. Knee pain is often caused by having your seat too low. You legs can't extend the range they need to causing your legs to pedal kind of to the side (this happened to my DH). Perhaps if you raise your seat some??
3. Ease the tension on your pedals. That should make clipping in and out much easier. Don't worry about the cleat becoming dislodged on a ride. My pedals are loose and I've never had it happen to me.

Keep us posted. Hope your legs/feet feel better soon!