I might chime in here with my single experience. My wife and I recently returned from Tokyo earlier this month with two guitars and a load of gifts, etc. I may not have all the numbers straight, but this may give you an idea. The US customs sheet said we were allowed $400 each duty free (total $800)...anything beyond that was supposed to be a 10% charge. Here's the poop:
http://www.customs.ustreas.gov/travel/travel.htm
Now that i look at the table there, it indicates 3%? We claimed $1800, so I was expecting to pay about $100. BTW, I don't get the idea that US Customs hires the brightest people. This poor old guy punched some numbers on a calculator, and then it took 2-3 ladies to get into the cash register. The grand total for duty came to $21. Go figure? I was pleasantly surprised. Maybe it was a fluke...either way, even with what I thought I was going to have to pay, it came out better that if I would have shipped even one of the guitars.
Rich is right...from what I have heard no customs on EMS. I asked a couple stores, and they were not willing to ship for me. However, you could always ship it yourself from Japan via EMS...you can find their locations on the web. In that case i'd get the shop you buy it from to package it...they did that for me on the guitar I checked as baggage.
All the best...keep us posted if you go! And see the sights while you're there.
Greg