My wife is having knee pain while on her road bike. I can feel the outside of her knee (right next to her knee cap) popping. It is only her left knee and it usually only seems to hurt when she spins in a light gear. She does not have this issue on her mountain bike or the spin class bikes. She had an x-ray done and saw a knee specialist who said it looked fine. He thought that it might be due to her inside thigh muscle being stronger than the outside. I'm guessing it is a fit issue.

Any suggestions on what adjustments we could try?

How different are her crank lengths between mtn and road? Maybe check pedal/shoe position and mess around with cleat placement to see if that helps.

I had some muscle imbalance issues, my gluteus medius was really weak and my gluteus maximus was strong, physical therapy solved that problem.