Personally I stopped fitting linkage stoppers on the servo arms a long time ago. Simply I found it easier to do adjustments on the exterior of the plane at the control horn mounted linkage stopper.
This allowed me to select another hole in the servo output arm without drilling, removing the servo, or even removing the pushrod by just removing the servo control arm move the pushrod to the new hole and refitting the servo output arm. It also allowed me a little more room around the servo, especially height.
As for selecting the required hole I just guess and fit the whole servo, pushrod, control horn arrangement and check for the required deflections. I then change hole selected if required, either on the servo output arm or on the control horn.
This is just what I do now for ALL of my builds. I find it more user friendly. You do what works best for you of course!