Can fore and aft issues cause similar pains as being too high or low on your "post"?
IE, I am familiar with pain front or rear of knee from having the height incorrect.
I just changed saddle from the stock one. Set my post height at 31" start point like I always do and go for a ride. I have the height within a 1/8" point that I feel is right, but one way and the front of my knee hurts, and the other the inside back hurts.
On fore and aft, the geometry on this bike is more crank forward than my roadie, but I still have "plumbline" down from the knee through big toe joint.
It could actually be that I haven't ridden Jack Squat for miles since Halloween too......(yathink?!?)