Sounds like you are doing well with PT. Having two knees are different stages must be rather interesting, especially for things like a bike. You can only do as much as the younger knee lets you. I'm glad your PT has some ideas for helpful, and I hope gentle, exercises.
For me, the night pains were, and still are, mostly positional. My right knee isn't fussy. My left, though, doesn't like it if during the night it bends even slightly to the side. Bending back is no problem. But if gravity pulls it even a little to the inside... well, Old Cranky Knee wakes up. And I wake up. For what it's worth, it has become lots easier to get back to sleep recently, so things do get better. Slowly sometimes, but better.