Can you do lunges, band work, step ups/downs, etc... without pain? How are your DLs, core work and glutes? The problem with the knee is that all sorts of other imbalances can show up as knee pain. Also, see if you can find a PT that specializes in sports.

Read this for some things to try to protect the knee: http://www.t-nation.com/free_online_article/sports_body_trai...