Clockmakers have what's called a "depthing tool" to set gear spacing properly. You can use Google images to get a picture of one.

Basically it consists of two shafts, each of which carries one of the gears. The shafts are carried on frames that are hinged together. The hinge is adjusted to provide the proper gear mesh. The ends of the shafts have points that can then be used to mark the workpiece with the exact spacing to produce proper mesh.

I'm glad you're finding the math programs useful. Almost all of them were written to address a real shop problem so there's very little fluff there.