I will be traveling to Japan in March and will be using an all Japan Rail pass for the extensive use of trains while we are there. Almost 30% of this travel will be using Shinkasen for long-haul trips between distant cities.
I am very concerned about having to acquire a Shinkasen ticket at the station on the day of travel, especially in the case of reserved seats. It would be a major imposition if I suddenly found I couldn't get a seat (or seats together) for the long travel routes in the middle of my trip.
Any ideas on how to avoid this potential problem?
I believe you have your question answered, but just to be clear, there are no train tickets with the rail pass. There are seat reservations you can make with an activated pass, and you can reserve seats up to a month in advance. You can easily check rail schedules, transfer info and fares on Hyperdia. Please note though that if on a rail pass, under "More Options" you should uncheck the Nozomi box since you cannot use that train with the pass.
March is not typically a very busy season, compared to the peak seasons like the end/start of the year, Golden Week, Obon, etc. There is no need to be so worried. But if you want to make seat reservations, you certainly can, and they are a free perk with the pass. If you do make seat reservations though, it does tie you down to a more restrictive schedule.
You didn't give your itinerary, but you might want to run it through this rail pass calculator to see if you actually make it pay off. You could save a lot of money on a rail pass, but if you travel too little or too slowly, you could lose money on a rail pass too.
Sorry I just reread your question and thought I may not have clearly answered your question.
You cannot get Shinkansen tickets online. You can order and receive a voucher online that you will have to personally redeem for your railpass at one of the major train stations after you arrive in Japan. You must aquire the voucher prior to entering the country.
March is a beautiful time to visit and possibly see the cherry blossoms in Japan! You should make your seat reservations in advance after activating your rail pass. This will dramatically increase your chances of keeping everyone together. If you are flying into Narita and plan to activate your rail pass there be aware that they don’t usually (I was able to when it was an off peak time) allow you to make more than a single reservation as they get quite busy as you can imagine. If you are in or near the Ueno area I would suggest that station to make the remaining seat reservations. I found Ueno station to be one of the least crowded especially when compared to Tokyo or Shinjuku stations. It sounds like you have already purchased your pass but if you haven’t already done so you may want to consider purchasing the green car upgrade. I always find the green cars less crowded and seats with footrest well worth the added expense.