It isn't hard to get around on the subway (although we were told to avoid rush hours - except as a cultural experience - very very crowded - and we did). All the subway station name signs - at least in Tokyo - were in English characters. It can sometimes be hard finding the correct exit at a large subway stop - there can be dozens of exits - but usually there's no harm even if you take the wrong exit (except maybe having to walk an extra block or two).

It's sometimes hard to find small restaurants - but the hard to find ones are hard to find whether or not you speak/read Japanese.

Overall - you're going to have some "Lost In Translation" moments - and get lost once in a while - but it's not like a Japanese tourist missing one particular exit on the Florida Turnpike and having to drive 50 miles out of his way to get to the next exit . My only advice would be to give yourself some extra time if you have to be somewhere at a specific time - or to take a cab. Otherwise - no problem getting somewhat lost and exploring. The city is super safe (clean too) - you don't have to worry about wandering into bad neighborhoods. And the people are very polite.

Customs shouldn't be an issue at all unless you're bringing in something other than normal tourist stuff (including duty free). Nor should getting to your hotel. Try to fly into Haneda if you can get a decent flight there - it's much closer to downtown than Narita.

I don't know anything about the phone stuff. I travel with my notebook - and that's where I get my info if necessary (note that just about any decent hotel concierge will help you with specific directions written in English and Japanese - you can show the Japanese to people if you get lost).

I'm probably much older than you are - and my only concern with our upcoming trip is how I'll feel with a 13 time zone difference! Robyn