Try this method: Center the control surface. I disconnect the control surface from the servo by removing the servo arm, then center the control surface by sandwiching it between two lengths of 1/8 ply and use a clamp each side (right and left) of the horizontal stab (if doing elevator for instance) I center the TX arms and trims, then center the servo arm so that it's perpendicular to the side of the servo. You may have to rotate the servo arm to select the right one. If it is off from perpendicular, you will introduce some slight amount of differential. Once everything is centered, replace the servo arms then remove the clamps.

Move the servo arm, using the TX, to full deflection and see how much it moves and measure it from the flat surface the plane is resting on. See if it deflects the same amount both up and down (it should) and see if your deflection measures ok. If not, make the appropriate mechanical adjustments. Try not to use the electronic end-points if you can manage to get things right with the mechanical adjustments. Your end points should remain at 100% so as to maintain resolution.

The important part is centering everything then measuring the throw.