Last time I went to Japan, we stayed in a few different hostels (Osaka and Tokyo). Decent budget, good place to meet other travelers, and usually not too far from a subway station. You can likely get help from the staff there as they usually speak some English. I definitely second getting a map that has both Japanese and English on it for Tokyo, particularly of the subway routes. With that, even if you wander around and get a little lost, as long as you find a train station, you'll be able to identify where you are and what routes you should take to get back. You can probably find a quick explanation video on how to buy the right subway tickets and how the transportation system works.
Japan is very safe--even the more dodgy areas are not really threatening. Just make sure to keep clear of staring at Yakuza members...usually men in suits and sunglasses and/or with tattoo sleeves. If you are going to Tokyo, make it point to go to Akihabara and spend a couple days checking out every little store in the area. There's lot of gaming goodies and hidden gems lying around.
As for ordering food, if you're adventurous, you can sit yourself down in a restaurant that has pictures for its food (quite a few show models of what they serve) and point at what you think you'd like. You may also find vending machines that produce a ticket that you hand to a counter for food--those sometimes have small pictures as well. One of my best adventures was stumbling upon a traditional yatai with a couple friends, not knowing a single Japanese word and having other customers at the stall buy us things to try. The stall only served eel. Just eel, ALL PARTS of the eel, cooked in different ways but mostly skewered. I've had regular eel before, but not the innards or the head. Suffice to say it was an interesting experience and I will still eat eel. This was at some part in Shinjuku, which is the biggest most maze-like area you'll find in Tokyo, but it's full of small surprises like that.
It's also not a bad idea to visit the fast food places like McD's and Wendy's--they have Japanese inspired items like tempura burgers. Mos Burger is another good place as they actually serve rice burgers: the bun is replaced with rice cakes instead. Coco Curry is a Japanese chain I adore, and they have pictures. It's Japanese curry with 10 levels of spiciness (you have to prove you've eaten certain levels before you can go up the charts), and you can choose whatever toppings you want added to the curry. If you're less adventurous, the convenient stores have a great selection of pre-made meals and interesting instant noodles that you can choose from, so you would at least know what you're getting most of the time.
Learning some common Japanese food dishes that you would like to try is also not a bad idea. You can then ask the servers if they have a particular type of dish, and if they don't you can always head elsewhere. If you stumble upon a Japanese bakery... just go in and buy everything that looks awesome. It will be awesome.
Protip: grocery stores slash their sushi prices at night, great time to pick up some deals for the next day or a late night snack.
So... if you're going to go, get a good map, an adventurous stomach, a wandering spirit, and you'll probably have a great time.
P.S. Lard is right that Osakans are friendlier--they are considered "too friendly" by most Japanese.