Julie, I think that the prehab is helping. I have taken the last two weeks off from lifting (partially thanks to a crazy hectic "now we're out of school for the summer" schedule) and just done the prehab exercises and some bodyweight stuff. Today I did a modified version of a Stage 3 workout--avoiding any of the squatting movements because they had been bugging my knees--and things went well. The knees are feeling pretty good tonight. I'll probably start back with some squats and lunges next week and see how they go.
Thanks again for the advice!