I also don't know him, not personally, that is, but I consider Mike a friend.

Unfortunately I can't find a way to link to the reply I was referring to so here's his Help-A-Gajin-Whos-Shitting-His-Pants-Cause-He-Has-No-Clue-About-How-To-Order-Food-In-A-Weird-Language (he does now) in all its glory (I hope, Mike, that you don't mind. But I couldn't imagine why you would and if somebody who's going to Japan anytime soon reads this. Let me assure you this is all you need if you want to eat well)

I still consider it one of the most incredible things ever happened to me on the internet.

(edited to add: The copy paste formatting is weird, sorry for that)

Anyway, here we go:

"I've gone to several sushi places in large centres, but nothing compares to my favourite place in my home town. It's kind of opposite to my initial gut feeling, but it makes sense in a strange way. In large cities, there are enough people to sustain mediocre restaurants. The top restaurants command really high prices, but you can survive if you are willing to charge less. In small towns, nobody has much money and they all eat at home. If you want to survive, you have to be amazing.
So if you find yourself in a small port town, chances are the local sushi restaurant will be amazing. The other really important thing to realise is that really, really great food is often available in incredibly unassuming places. The restaurant will be 50 years old, will be onto it's third generation of master, and will be falling apart on the outside. But the food will be incredible. So it's super hard to tell where to go.
A couple of things might help. First you should know a few kanji: 営業中 means "open for business". 準備中 means "preparing" (not open at the moment). The easiest way to distinguish it is to look at the first character. If it looks like a fat guy with his hair on fire, that's open :-)
Next, quite a lot of great eating establishments are also drinking establishments. Especially if you want to eat and drink at the same time (which I recommend highly). The thing to look for is 居酒屋 (izakaya -- bar/pub). Not sure how to remember it. Write it on your hand :-). People will be impressed if they see it! Often this will be written on an orange paper lantern outside the establishment. Stay away from things called "pub" or "snack". Those are drinking establishments, but are really hostess clubs and the food is terrible.
Another thing to look for is a noren. Here you can see an image of one [0]. When shops are in business, the noren will be displayed out like that. When they are closed, they will either be taken down, or displayed behind a closed window.
The best thing to do to find good restaurants is to ask for recommendations from the hotel where you are staying. It's important to indicate that you are looking for an actually good place and not one catering to tourists. It may be slightly difficult to communicate that. The main concern is that because you don't speak Japanese, you won't be comfortable in a Japanese establishment -- especially if you can't read the menu. If you can't manage to get an answer from the hotel staff (often they are afraid to make a mistake), the way to go is simply to have courage and wander into likely looking establishments.
Extremely good restaurants don't cater to tourists. They won't have menus with pictures on them. They won't won't won't have menus with English. They won't speak English. They spend all of their time thinking about food, not sales. You have to break down the barrier with your own courage. It'll be fine, don't worry :-) And if it isn't, they will be very polite as they usher you out the door ;-).
Some very quick useful Japanese: When you enter, it's useful to say, "Aite imasuka?", which means "Are you open?". If they cross their arms in an X pattern, it means it's no good. Otherwise it's probably OK :-) If they are willing to seat you they will say, "Nan me sama?" (How many people?). Just hold up the appropriate number of fingers. Again, if it's no good, they will cross their arms in an X pattern.
When ordering, draft beer is "Nama". Sake is "Nihonshu". Something stronger is "Shochu". But you can probably get away with ordering "Whiskey" or "Wine", etc. Carbonated fruit flavoured alcoholic drinks are called "Sawaa" (sour) or "Chuhai". If you want to stay away from alcohol, the mainstay is usually "ooloncha" (oolong tea). You can also order "cora" (cola), etc.
For food, just ask for a suggestion: "Osusume wa nan desu ka?" (What is your recommendation). Whatever they say, respond with "Hai. Onegai shimasu". ("Yes, please") It'll be great. Even if they just asked you a question, by responding with "Yes, please" you will establish that you have no freaking clue what they are saying and that they should just give you food.
As you eat, it's good to smile and remark "Oishii!" (Delicious!). Shop owners are very concerned when foreigners enter because they don't know how to please you. If you are visibly happy, they will also be happy. It diffuses a lot of problems. Usually they will give you a lot of special free food (or sometimes they will give you a lot of special, expensive food that you will pay for ;-) But they will love you!) Unless you have food allergies do not ask for substitutions or customisation!!!!! Japanese restaurants can't deal with this. The server's brain will melt. If you press the subject, they will sadly go back to the kitchen where the chef's brain will melt. After a very long time, they will come back and ask what they can possibly do. If you press the subject, they will probably cry. Don't do it!
If you have an allergy, say "Arerugi nan desu!" (I have an allergy) and try to describe it as best as possible (Best to have it printed in Japanese before you go so you can flash it to them).
Since you were asking about sushi, the kanji for sushi is 寿司. The best sushi restaurants will not put that on a sign because they are the best sushi restaurant in the area and everybody knows it's a sushi restaurant (which is why you need to get a recommendation). Unless you want to try kaiten shushi (conveyor belt sushi -- which is actually quite fun, despite the terrible food) say away from 回転寿司 restaurants. Again, if it has photographs of food, or English menus, it might be good, but it won't be at the top. Also, don't look for modern, glitzy, fancy restaurants. Look for "It seems to have been around since 1950 and they haven't painted the exterior once". But the inside will be nice.
Other than than, just relax, have courage and enjoy your trip! The food here is amazing virtually everywhere. On a 3 1/2 week trip you will see and do a lot of great stuff (I envy you going up to Hokkaido -- especially by train). Keep in mind that every small town is incredibly proud of its local produce and cuisine. They will want to impress you with it. Just take it in and appreciate it. If you do, people will respond with more kindness than you can imagine.
Hope that helps!"