Not much comes from the factory in the toolkit-two tyre levers,a spark plug wrench,two screwdrivers (philips and flat), and four open-end wrenches,and a pouch to hold them. A clutch cable and front brake cable are supplied with a new bike,too,along with a spare inner tube. This is just the bare minimum for tools-many guys carry much more with them.
A good idea would be to get a parts manual, and the service manual for your bike-if it has been sitting that long with so few miles, you will probably have to be changing some seals, or cleaning out the carb (if you haven't done this yet)