Pain in knees and hip

This doesn't sound right. It's hard to tell what the problem is - are you bending your knees too much? Are you hyper-straightening them? Are they very sensitive to any shift from perfectly neutral (it's hard to get the knees perfectly aligned lying on the side)? Do you have a way of lying on the side that doesn't cause pain? If you do, go back to that and then add just one ingredient at a time to see where the problem is. Try just adding some extra length into your spine and nothing else for one night and see what happens. If you don't have any pain-free way to lie on your side, I recommend going back to stretchlying on your back, continuing to work with your leg alignment in sitting, then standing, then walking and periodically in this process try sidestretchlying and see if your body now tolerates it. It sometimes takes the legs a while to unwind...

As for your hips, same as above, but here a towel roll in your waist can help if you have a narrow waist and wider hips. Keep us posted on your progress!