While looking for a fitter you can do some modification that may help with the knees. Peter White has an excellent site for doing a fit and can be found at How to Fit a Bicycle. Focus on setting up your fore-aft and seat height correctly as these have a big impact on knee pressure/pain. My knees are sensitive to 2mm in height adjustment when cycling over 25 miles.

Also when I first got started and increased the miles and hills my IT band would cause my knees to ache badly finally to the point of having trouble walking and no amount of stretching would fix it. If you have a foam roller, I highly recommend you try that to free up any adhesions in the IT band and really the muscles attached to the band (DON'T Foam-Roll Your IT Band! | ASM Wellness).