How much should a 2 week trip to Japan cost for two people?

Question:

Like comprehensive... including food, transportation, plane tickets, hotels, spending money etc etc

I'm doing a little math myself and it keeps coming up to about 10,000 with one week guided tour of south Japan and plane tickets. Does that seem right?

Answer:

The airfare quoted is about right, but you don't have to spend the wildly high amounts for hotels and other things others quoted unless you want to. There are far less expensive budget accommodations if you want, and you can eat modestly for about USD13 each at an inexpensive restaurant, or for even less if you get a bento or groceries at a market.
But you don't say where you are going, so there are a lot of variables. If you want to go all over the country, consider getting a JR Rail Pass before you arrive in Japan (see www.japanrailpass.net). Or you can get a regional JR Pass for certain areas after you arrive. And you can get a subway day pass for about 1000 yen in many major cities. And there are overnight buses between Tokyo and Osaka or Kyoto, for example.
A few cheaper places to stay are at
www.newkoyo.com
www.sakura-hotel.co.jp
www.shrek-watta-house.com
www.tamaryokan.com
www.tokyoryokan.com
www.jyh.or.jp/english/
www2.dango.ne.jp/kimi/ryokan.html
www.libertyhouse.gr.jp
www.juyoh.co.jp/
www.palace-japan.com/english/index.htm…
www.palacesidehotel.co.jp
www.o-e-h.com
www.Kyotojp.com
www.hotel-toyo.jp/
www.toyoko-inn.com/eng/
www.superhoteljapan.com/en/
In fact if you have never stayed in a Japanese inn (ryokan) before, I recommend it at least a night just for the experience.
As for shopping, that is solely up to you. You can spend a couple of dollars here and there for some small mementos, or go all out where the sky is the limit. Again, it's up to you. But don't believe all the scare stories that you need thousands and thousands of dollars - if you want somewhere to stay that is decent yet clean, you easily can.
See www.jnto.go.jp for a lot of tourist info.