For all practical purposes, Pasmo and Suica are the same in the greater Tokyo area, but Suica is valid in more parts of Japan. (The list has expanded a lot in the past couple of years.) Having a card eliminates the guesswork in transit fares, because the fare is automatically deducted as you swipe the card going onto and leaving the platform.
I'm of the opinion that first-time visitors to Japan should not fly domestically unless they have to cover huge distances in a short time. High-speed rail is one of the quintessential Japanese experiences, and it gives you a glimpse of what Japan looks like between major cities. Even landing in Tokyo one afternoon and making a noon-time meeting in Hiroshima the next day is no problem on the Shinkansen, even if you have a JR Pass, can't ride the Nozomi, and have to change trains at Shin-Osaka.
Japan is quite affordable if you don't need a luxury hotel and gourmet meals. Stay in business hotels in the cities (US$100 or less, as little as US$50 in the smaller cities, for a bare-bones single, sometimes with breakfast) and minshuku (low-cost ryokan-style rooms in family homes) in the country. Eat in the countless mom-and-pop, hole-in-the-wall restaurants that line the streets of every city.
Yes, you can drink the tap water.
That yellowish-tan liquid that some restaurants will serve you in the summer is iced mugi-cha, or barley tea. It's kind of bitter but refreshing if you can develop a taste for it.
Don't order coffee or black tea in a restaurant unless it's specifically advertised as part of the meal. It will cost you. For a quick caffeine pick-me-up, go to a fast food outlet, a real coffee shop, or a vending machine (hot canned coffee in the winter, cold canned coffee in the summer).
If you go sightseeing in the winter, wear thick socks. You have to take your shoes off to visit temples, and you will be sorry if you do this while wearing thin socks.
Nowadays, washrooms in the cities usually offer a choice between Asian-style and Western-style toilets, but small towns and minshuku or ryokan may have only the Asian style. Fortunately, the aging of Japan's population has prompted the installation of handrails in the Asian-style stalls, so that Western visitors who have not perfected their deep knee bend techniques can do what needs to be done without falling over.
However, it is rare to find a washroom that has hot water AND soap AND paper towels. Carrying moist wipes (wetto tisshuu) or hand sanitizer is a good idea.
Above all, if you land at NRT, do NOT take a cab to the central city unless you do not flinch at the price of a 5-star hotel room. The airport is 60km (40 miles) out of town. Take one of the rail options or, if one goes to or near your hotel, the Limousine Bus, for US$30 max.
The luggage-forwarding service is one of my favorite things about Japan.
Japan is only about the size of California. You can take easy day trips from both Tokyo and Kyoto, so you can go several days without changing hotels. Osaka, Kyoto, Nara, and Kobe are all within day trip distance of one another (e.g. Nara is 30 minutes from Kyoto), and you can range even farther afield. I once took a group of students on a day trip to Hida-Takayama from Kyoto.
Read up on Japanese culture and history before you go. Otherwise, all the shrines, temples, and castles will look alike. See if you can find a copy of Gateway to Japan. Its descriptions of hotels and restaurants and prices in general are ridiculously out of date, but no book that I know of provides a better overview of things like who all those Buddhist statues are or why the Tokugawas are important historical figures.