JR passes are not worth it unless you are using at least 3 long distance trains within the period the pass is valid for. They are to restrictive as to what lines can be used within the cities.
Get an IC card (from a ticket vending machine at a station. Most machines have an English mode). There are 2 available in Tokyo, Pasmo and Suica, both of which are fully interchangeable (ie, you can use Suica where pasmo is asked for, etc). They can also be used in place of IC cards from other parts of Japan (eg, you can use Suica - issued by JR East, in place of ICOCA - issued by JR West in Osaka). You should be able to use Suica for any local trains and buses in Iiyama/Nozawa.
Keisei Skyliner stops at 2 stations in Tokyo. Nippori, which is the same station as JR and makes connections to the JR local Tokyo network quite easy, and Keisei-Ueno, which is a short walk away from the main Ueno station.
Only the Hakutaka service on the Hokuriku Shinkansen stops at Iiyama, and not all of those do. You may need to get off at Nagano and change to the Iiyama line.
You can't use Suica for the Skinkansen as they are reserved seats and most trains with reserved seats involve a seat fee and paper tickets (though there are some trains where you can use an IC card for the base fare and pay the reserved seat surcharge on board when they come check tickets).
Go to a JR ticket office at Tokyo or Ueno station and get the Shinkansen tickets. Easiest thing would be to write down which train, dates and destination you want to show the agent. It doesn't have to be the same day.
I got return Shinagawa-Toyohashi Tōkaidō Shinkansen tickets (day trip) at Tokyo Station 4 days before the trip last year.
