It's awesome to eat in Japan. There's quality eats to be had at all tiers, not just top tier. Best food chain in the world.
A few words about reservations: Outside of fast food or ramen, it helps to have reservations at all restaurants beforehand. Even if you're en route to an eatery on a whim, give them a call and tell them you're coming. It's a respect thing, and will be much appreciated by your hosts.
If you are not a Japanese speaker, ask a Japanese speaker to help make rezzies. This goes especially for higher-end places. For many tourists, this means asking your hotel concierge to help you, which is fine. If you are dining at a place where the reservation is tough to procure, you may need to ask your hotel concierge (or Japanese-speaking friend) a few months ahead to book it for you. If that is unsuccessful, an American Express concierge (if you have an AmEx card) can often assist.
Tipping: None! Your bill is your final bill. Tipping is discouraged in Japan - no tipping in restaurants, no tipping in taxis. The only possible exception to this rule is the bellboy who carries your luggage, and even that is not a hard rule.
Getting around: In Tokyo, prepare to walk from station to station. A lot. The Tokyo public transport system is truly a marvel of modern human design. If you're gonna be in Tokyo for a 5-day stretch, I'd suggest you get a one-week all-inclusive card (e.g. Suica) so you don't have to queue too much. Walking is great. It's what keeps obesity at bay in Japanese society, and many visitors find that they can eat as much as they want and not gain weight in Japan due to all that walking (that, and the fact you're eating mostly food made with "real" ingredients, and less processing). Shinkansen: Get the green pass if you plan on traveling quite a bit on the Shinkansen. It can only be purchased from outside Japan, and is activated once you are in Japan. The Shinkansen bento box is another fond food memory when going on the Shinkansen - Buy them at the train station before you depart.
On getting lost: Japan is probably THE safest country to get lost in on this planet. Some of my best food memories in Japan have come from getting lost, and finding that local restaurant with that amazing local specialty. The local street addresses are often mysterious, and you might narrow down your destination to the block, but have to walk around it like 3 or 4 times before you find the actual address. If you truly find yourself flummoxed, however, one possible thing to do is find the Koban (local constabulary/police) box or kiosk and ask the police for directions. The friendly cops know their assigned neighborhood extremely well and can assist you. Very often, your destination restaurant will be on the 3rd or 4th floor (we Angelenos are often not used to this fact of Japanese life).
My recommendations for Tokyo: Don't ignore the depachikas. Grab a hot corn soup from the vending machines. Visit Lawson and buy an onigiri to munch on. By the way, all the rice (even the rice used to make the Lawson onigiri) is exquisite in Japan. Eat at a Yoshinoya and marvel at how great the beef tastes. GO to McDonald's and try a McEbi. Go to a fruit parlour (Sembikiya is great) and try a slice of musk melon. The Japanese breakfast buffet at Tokyo Station Hotel is incredible.
Sushi: Sawada in Ginza (it is almost holy to me), Kozasa (not sure I should 'out' this place, but what the hell), Sukiyabashi Jiro in Roppongi Hills (AKA his second son's restaurant). Try kujira nigiri (Asakusa has many kaitenzushi places where this is sold). Try the "standing only" sushi bars in the business districts. Try basashi nigiri. Visit Tsukiji Market - Marvel at how there is no fishy odor at all, despite it being the largest seafood wholesale marketplace on the planet.
Noodles: Rokurinsha (on Ramen Street at Tokyo Station) for tsukemen.
Tonkatsu: I love the Tokyo X hybrid pork at Maisen.
Kyoto: Are you staying at a ryokan? If so, the in-house kaiseki should be very authentic and good.
Osaka: Informal street food: Yakisoba, takoyaki, all washed down with lots of beer.
Getting so hungry... Take me with you!