Uh oh, don't scare me with the knee pain!! actually that's my biggest fear that my knees will start aching and popping because my kneecap dislocated a few years ago and neither it nor the other one has been the same since. It probably is the relaxin causing it for you now, because when those ligaments loosen up and allow the kneecap to slip and slide, it causes pain and knee popping. Also the increased weight is putting more pressure on your knees.
Part of my phys. therapy was strengthening the quad muscles in the thigh, so everytime I get the knee pains again, I work those quads--they help rein in the ligaments that hold the kneecap in place. Maybe this will help you?
Oh yeah, and for knee and hip pain my chiro suggested wearing shoes with good arch support like birkenstocks for example--because when your feet are flat (as happens in late pregnancy), your knees bend more inwards when you walk and all the weight just hits you straight on in the knees. The lack of balance also upsets the hips. Since I got my birks earlier in the pregnancy my hip pain has disappeared and I haven't had a recurrence of knee pains.