Public toliets are not a problem in Japan. It's much easier to deal with bodily functions in Tokyo than say, New York. The subways & train stations still have toliets, unlike in many American cities.
Hanzoemon is a convenient spot to get in and out of. I've only changed trains there, so i can't give you all that much advice. You'll be seeing the cherry blossoms around the imperial palazzo. You'll also be seeing hordes of drunks. Have fun!
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