Hi there,
Did you have a time you wish to travel to Kyoto into mind? Haneda airport is very small and waiting there until 11 a.m. would become boring quickly.
I would suggest exchanging your Pass at Tokyo Station, which opens at 7.30.
To get to Tokyo station, take the mono rail from Haneda Airport to the last stop Hamamatsucho and tranfer there to the Yamamote line (bound for Tokyo and Ueno. Tokyo is three stops away.
There are a couple of things you can do here to enjoy a little of Tokyo. The first is a walk to the imperial palace, it is very close and the castle gardens are very lovely when the weather is good.
An other is to head to Ginza, well known for upper class shopping and is home to some of the most expansive brands in the world.
You can take the Shinkansen directly from Tokyo station once you head to Kyoto, so be sure to enjoy the ride. Ask for a C and D seat when you mean seat reservations and you may be able to see Mount Fuji on your right side if the weather is good!
Enjoy Japan!
Daniel