Here's the thing about tokyo restaurants. You can't just walk into decent places expecting a table, especially at dinner. Make reservations or you'll end up eating convenience store food.

Most places don't take phone reservations in english. Use your hotel concierge or book through opentable/tabelog if they're listed. Some high-end spots require japanese speakers to call - that's not discrimination, it's logistics.

Here's what not to do: don't show up late, don't ask to modify dishes, don't expect english menus everywhere. Follow their system and you'll eat incredibly well.