i would change about $500 to yen at your own bank before you fly. the equivalent in Yen will be relatively few bills so its not like you'll have an obvious cash bulge that'll be tempting would be pickpockets.
that much will keep you comfortable enough for the first few days so you dont have to rush out and find a bank. (head to shibuya's citibank for quick and easy cash withdrawals using a visa electron or credit card. just ask for the KFC i think it was, someone correct me if i'm wrong, its just after that, 5 mins from shibuya station).
its safe, but a friend might make your trip a bit more fun and unpredictable, depending on the friend of course.
you can point at things with your fingers, you dont have to carry a handkerchief, and you dont have to be absolutely silent on the train. those rules are more for the "gaijin that wants to be a japanese" type of visitor. honestly, i have no idea where they get funny ideas like that.
cookies would be nice gifts, i certainly would welcome a good batch of cookies
