I have a similar issue with my stable of rides. All of the measurements are about the same, but a couple of the bikes when I take on longer rides above 60 miles, I have signifcant pain post ride.

I've deduced that the majority of this is due to differences in frame geometry - while the handlebar to saddle measurement may be the same - the angle of my hip to torso is not. Or my foot angle on the pedal might be different through the pedal stroke.

My solution is to follow the measurement s as a guideline and adjust and optimize for comfort.