Can anyone you tell me how to tell the difference between a long shaft and a short shaft motor? How long is a standard short shaft?

The standard, known as "short shaft" is 15"; the long shaft is 20". When I buy a skiff I choose the higher transom option, so I also choose a long shaft outboard, which I also can use on lower transom rental skiffs when I do not have my boat with me.

Where would I mesure from? Is that from top to bottom or from the bottom of the engine cowl to the prop? Thanks

On my old Mercury here at home it is 20" from the bottom of the shift lever connection to the anti-ventilation plate (i. e., the distance from the top of the shaft to the anti-ventilation plate). My new Honda is on my boat berthed elswhere so I do not know offhand how the 20" shaft on it can best be described for you.