I would think the set up could best standardized in the same fashion as a job router, with steps being given a number.
If a step like "Align chuck jaws" would need to fundamentally change from one tool to the next, it could be broken down by digits, name or number of tool, etc.
A database could hold a master list of all of these, and process steps only belonging to "Sammy" (tool name) could be listed along with generic steps (steps that do not differ from one tool to the next).
Step
1. Select drill bit
2. Insert into chuck
3. Align chuck jaws
3Sammy. Align chuck jaws with a .010 feeler gage; all jaws must touch the curring tool shaft to achieve even pressure and a straight trajectory. Tighten to 25 inch lbs using a .250" allen head torque wrench.
Once a tool set up is established, it could be saved and just edited later.
Disclaimer: this is how I imagine setting up a system in a job shop, using rudimentary tools like Excel or Access. Your needs may vary, and manufacturing flow software almost surely will be more sophisticated, it seems to me.