Also a Check List:

* Passport and Visa
* Airplane Tickets
* Japan Railpass purchasing order
* Traveler's check
* Japanese yen in cash if possible
* Travel Insurance
* Credit cards
* Photocopy of all these documents
* Small suitcase or extra bags
* Camera (film is cheap in Japan)
* Umbrella
* Small calculator
* Dictionary (Japanese Conversation book) / Guidebook
* Sewing set
* Walking shoes
* First Aid Kit / Prescription / OTC Medicine
* Alarm clock
* Glasses and Contact lenses
* Jackets / Night wear / Socks / Underwear
* Shaver (cordless would be good)
* Laptop if you need
* Plastic bags (can be trash bags)
* Pen / Memo note
* Cosmetics and your amenities

And some more info for you:

If you know these key Japanese customs, you?ll get closer to the locals and see beneath the surface of Japan.

1. Addressing Someone, Respect

Bowing is nothing less than an art form in Japan, respect pounded into children?s heads from the moment they enter school. For tourists, a simple inclination of the head or an attempt at a bow at the waist will usually suffice.
The duration and inclination of the bow is proportionate to the elevation of the person you?re addressing.

2. Table Manners

Some simple bullet points here:

- If you?re with a dinner party and receive drinks, wait before raising the glass to your lips. Everyone will be served, and someone will take the lead, make a speech, raise his drink, and yell ?kampai!? (cheers).

- You will receive a small wet cloth at most Japanese restaurants. Use this to wash your hands before eating, then carefully fold it and set it aside on the table. Do not use it as a napkin, or to touch any part of your face.

- Slurping noodles or making loud noises while eating is OK! In fact, slurping hot food like ramen is polite, to show you are enjoying it.

- You may raise bowls to your mouth to make it easier to eat with chopsticks, especially bowls of rice.

- Just before digging in, whether it be a seven-course dinner or a sample at a supermarket, it?s polite to say ?itadakimasu? (I will receive).

3. No Tipping

There is no tipping in any situation in Japan ? cabs, restaurants, personal care. To tip someone is actually a little insulting; the services you?ve asked for are covered by the price given, so why pay more?

If you are in a large area like Tokyo and can?t speak any Japanese, a waiter or waitress might take the extra money you happen to leave rather than force themselves to deal with the awkward situation of explaining the concept of no tipping in broken English.

Just remind yourself: a price is a price.

As a side note I wouldn't bother going to Yakushi-ji and Toshodai-ji; I found both were over-rated and rather uninspiring. The latter is also undergoing an extensive reconstruction project. Houryu-Ji is worth it for the fact it's the oldest wooden structure in Japan which is some achievement considering how many temples have burnt down several times throughout their long history.

Heijo-kyo palace is a little out the way from central Nara and if I'm deadly honest I found it disappointing. The whole building is a reconstruction from the ground up and consequently it failed to convey a sense of antiquity. It's kind of in the middle of nowhere too but you can see it from the train if you ride the kintestu line to Nara koen.

Anyway, that's enough from me. Have fun on your trip and don't worry too much about manners etc. As long as you weren't born in a barn there is very little you could do that would upset them.

Thanks again for the information. I'll keep the suggestions about Nara in mind as I make plans.

Today I got the "exchange vouchers" for the JR Rail pass, and I'd like to mention that these passes are not something you can just order online at the last minute: here in the US, they have to be ordered in advance so the dealer can Fedex you the vouchers. There's only a handful of places that provide this service, so don't wait too long before you go. I got mine from JTB in Honolulu and it still took 4 days.
Then, as you may know, you take these vouchers to a JR station where they can exchange them for "real" rail passes.