Chondromalacia runners knee in a non runner?

Rheumatologist mentioned I had it in both knees after I described the type of pain. For me it seems to go away and then return every month or so. This is almost with no running as a result of plantar facitiis for the last few years. ( bike and pool only )The calves constantly twitch as well. I'm thinking the pf made legs weak and imbalanced. Or maybe orthotics changed something?I really don't want surgery, does anyone do specific stretching strengthening or other?