Knees Hurting??
Try strengthening your GLUTES!! Don't over do the quads and knees as you are trying to work those legs. Engage more of the Gluteal and hip muscles for less wear and tear on the knees. Grab a trainer and talk "glutes" as you figure out what moves target the biggest muscles you have without causing your knees to hurt.
Exercises To Try:
TRX Squat
Hanging(modified) Deadlift
Mini-band work
Hip Extension
Leg Press positioned with high heel
Hip Bridges (loaded/unloaded)
