I'd back off before it gets worst. Cut down on squats, leg extensions, and even the stair master as it's not making them feel any better. Also a good warm up followed by stretching before your weight training and even before cardio is helpful. Bodybuilders like Schwarzenegger would do light weight, high rep sets to help lubricate (warm up) as they put it, their joints before their workout. Taking from their insight, you can warm up your legs by doing light weight sets of leg extensions.

Congratulations on your weight loss by the way.