Thanks for all the advice everyone. I'm doing several things to help combat this now:

1) Working on perfecting some of the typical ITB stretches and, more generally, all stretches. I'll work on doing them several times per day.

2) I'm going to ice my knees briefly after any workouts or rides.

3) I will follow the steps outlined in several posts above to try and adjust cleat positioning, etc. before my short rides on Thursday and this weekend. If things don't improve, I will follow through with the professional fitting next week.

4) I will take it easy on hills and try to improve my pedaling (and spin at a higher RPM than before).

5) I will attempt to find another orthopedic doctor/surgeon, especially one with an emphasis in sports-related injuries. A second opinion is definitely a must.

6) I will continue with my purchase of the new, better fit cycling shoes and potentially explore insoles/orthotics.

7) I will hold off on the Bebop pedal purchase until I have a better idea of what's going on and how my current fitting is affecting things (and because I'm still leery of buying from a no-return-once-opened online store when I'm not sure I can shave my shoes down to fit the cleats).

I think that generally sounds like a good plan. I hope things get figured out. I really don't want to miss out on the cycling season. Thanks again, everyone!