I just went through something like this. Had a bike that worked pretty well for me, but bought new shoes, pedals, and had a total fitting at the same time. LOVED several things about the newer fit (more aero, delighted that my back was happy with the lower position, etc.).

BUT, knee pain that I have never had on the bike before. Messed with everything from cleat width, angle, shimming, etc. Saddle fore/aft, etc.

Finally, I am back to the old shoes/pedals/fit...and knee pain is slowly going away. We just never did figure out exactly what part it was...as everything like plumb lines and so forth seemed to be "OK."

I still would like to make some adjustments and see about the new shoes, and a more aggressive bike...but, it is more important to me to just be able to get out and ride! So...back to the old position/fit.

Sorry...kinda long winded...just wanting to affirm that even small seat changes can make a big difference in knee comfort, and it might make sense to just put the bike back to where it was comfortable.