if you've got the time and money, going to an experienced professional fitter would be worth it. there are so many variables that can impact your knees (foot position inside your shoes (arch support), cleat position, float, stance width, seat height, seat fore/aft, pelvis angle, etc.) and having a trained eye take a look at each of the variables will be much more helpful than trying random things without having a direct understanding of how it impacts the other variables and ultimately your knees.

is a "pro fit" gauranteed to fix your knees? no. but if the time and money are available, it's worth it. imo.