We recently returned from 2 1/2 weeks in Japan – Tokyo/Osaka/Kyoto. Our first trip. And I have some observations as a first time traveler which might be useful if you're planning a first trip.
First - the major cities in Japan are really, really big. Osaka is perhaps the size of New York - but metro Tokyo - with a population of over 35 million - is huge. Travel distances can be formidable - and travel can be difficult during rush hours. So don't get your heart set on some restaurant you heard about that's on the other end of town from wherever you are. I've heard there are 100,000 restaurants in Tokyo. There are lots and lots of good ones - and quite a few great ones. Pick places that are close to where you are.
Second - especially at the higher end - lunch is frequently a bargain compared to dinner. So look at lunches. Won't be a problem for most visitors from places like the east coast of the United States for the first week. You'll be starving at noon for a dinner-like meal - and asleep well before a fashionable dinner dining time.
Third - for English speakers - there may be a beaten tourist path - but we didn't find it. English isn't spoken at most of the restaurants we dined at. My husband studied Japanese for a year before this trip (he's good at languages) - and I think it's a good investment of time to learn at least a bit before you go. Invest in a few books for eating - like Robb Satterwhite's "What's What in Japanese Restaurants" and Richard Hosking's "Dictionary of Japanese Food".
If you don't speak Japanese – all is not lost. There are thousands of restaurants with "plastic food" in the windows. Lots are very very nice. You can just point at meal 1, 2 or 3 and off you go. At high end restaurants – there will frequently be 1 – or perhaps a few "set menus". If you know you're going to a high end restaurant – talk with the concierge at your hotel about choosing your menu in advance if there are choices so you'll know what you're getting for $100 - $200 or $300. Your concierge can phone the restaurant in advance and let it know what menu you want.
And do not hesitate to take advantage of anyone you know - or think you might want to meet - when dining. Invite anyone and everyone who lives in Japan to dine with you. You won't regret it. We dined with many people. Including the son of a friend of ours who lives in northeast Tokyo (and his family). He took us to his "local" Chinese restaurant - owned by "Iron Chef Chinese" Chen. Great fun. If you guess a place like this would be a tourist place - guess again. I'm glad he and his wife spoke fluent Japanese.
Fourth - I recommend the "department store food basements" for sampling various kinds of foods. Although if you don't speak any Japanese - you probably won't be able to find out what you're eating unless you can identify it by sight. The food basements are also great for take-out on nights when you're too tired to go to a restaurant. The food basements are simply amazing - a tourist attraction in their own right. I could have spent days in them. They are one of the things I miss most about Japan now that I'm home.
Fifth - we encountered a huge number of incredibly friendly helpful people at restaurants (both chefs and staff). What we couldn't communicate in terms of spoken language - we did with hand signs (like we'll take one of what he's having – pointing at the person sitting next to you). Note that this isn't recommended at very high end restaurants – many of which are small places where you are served at counters - when they're busy (and all we went to were busy). For these restaurants - I recommend inviting a friend who speaks fluent Japanese to join you for dinner

. Robyn