Update 2015-02-05
Update 2015-02-05: I think most of the benefit comed from the stretches and exercises. When I've been lazy and stopped doing them my knees have started hurting again, and then they get better when I start again. I've also stopped doing much of the other things on the list, so it probably wasn't them. It's hard to say for sure with just n=1 and no control, though.