Knee Pain

The pain I've got is below the knee on the inside, which is in line with Pes anserinus isn't it? What is PFJS? Since I've had the wedges, started stretching and have had insoles I've noticed a difference.

Pain is still there but not as bad, does this mean It'll eventually disappear over time?

The pain location could be pes anserinus but this would be an unusual cause of pain in the ways you describe. PFJS is patellofemoral joint syndrome (knee cap involvement). If you correct your biomechanics and riding position and allow your knee to settle then hopefully you will be symptoms free.