You might find you need to sort out your bike setup a little. It took me a lot of tweaking to minimise my knee pain. I ended up putting some orthotics in my MTB shoes as well as I noticed on my weaker site I was excessively rotating my leg inwards during the push down on the crank. That was causing a torsion in my knee and then result was FAB.

It could also be an issue arising from the back that is causing a dysfunction in your gluteals and there the knee is a secondary problem. The popint here it to get your physio to check the mobility in your low back. The ITB is just a fascial component from the glutes and TFL so stretching/releasing them might be useful.

Are you using SPD's/clips or are you more of a downhiller?