Agree with the above. Patellofemoral dysfunction is common after patella tendon graft ACL recon's. This would need a total approach to his biomechanics. I would get the stability and mobility of the ankle and hip/pelvis right first, otherwise anything you achieve for the knee will be short term.

If you aren't confident with assessing functional biomechanics I would suggest checking out Gary Gray's functional movement screen - www.functionalmovement.com

Kevin