The difference between the "effective stroke length" and "surface stroke length" is rod stretch. If a long, small rod string has a stretch of 30 inches between the bottom of stroke and the top of stroke then with a 40-inch surface stroke length you would have an effective stroke of 10 inches.
Any competent pump-design program should be able to provide this number. There really isn't a rule of thumb that I've ever heard to get a Kentucky Windage estimate of stretch since every size, grade, material, and length of rods has its own stretch coefficient.
David