Yep. Due to wear and manufacturing tolerances, a .020" point gap isn't necessarily going mean that it's properly timed. Connect an ohmmeter to the the points such that the resistance is 0 when the points are closed and infinity when they are open. Turn the flywheel in the direction of normal rotation. When the points just start to break (the resistance will waver before going to infinity) the "S" mark will be under the roll pin in a KT-17 or in the sight hole in a K-series. The gap may vary quite a bit from the .020" spec.

Ignition Timing
 

Thanks Matt you said it better then I did for all who don't have a Ohm Meter you can use a simple 12 volt bulb & socket with two leads and alligator clips conected to the points and ground when bulb lites at the proper timing mark you are good to go. Turn on Ignition switch first motor doesn't have to be running this is called static timing the engine. turn engine over by hand slow. Read your manual for proper fireing mark. I don't know if the S mark is the fire Mark on all Cubs.

Timing
 

Understanding the "timing mark" in the manual is not real clear. I have a meter to use and when I rotate the engine looking at flywheel end, rotating clockwise, when the points just start to break or break there are to marks on the flywhhel. "TDC" and "S". There is a rollpin on the side of engine block for position of those marks to be in relation to roll pin. Manual says the "S" should be "just opposite" of the rollpin when points break.Do the mean just past when traveling clockwise?

According to Matt who knows your motor the S mark will be under the roll pin. Hope this helps

To further clarify...this is what you want: