Originally Posted by
msb0b
If you worried about not being able to book tickets around the New Year, you should consider putting the Tokyo portion at the end of the trip. Personally, I think doing the trekking up front and then have some time to wind down at the end works better. You can also use the time to pick up gifts and souvenirs, especially on the first, when the stores sell fukubukuro.
I've been wondering about booking situation during the New Year period which this year could stretch from Saturday 26th to Sunday 3rd. Obviously it isn't practical to avoid travel between these dates but 1st January is apparently a good day for travel since most Japanese don't travel on 1st. Trains out of Tokyo (and other big cities) tend to be crowded before the New Year and trains in the opposite direction are crowded after the New Year.
Seat reservations for Shinkansen and other long-distance trains start one month before the date of travel (one week earlier for online reservation) but for the New Year period advance reservation sometimes starts earlier. By the time the OP arrives in Japan not all seats will have gone (based on reports from previous years) but seats on some popular trains may have been sold out. Based on last year's reports busiest days/times would be the morning of 30th (away from cities) and the afternoon of 3rd (towards cities).
It would be best to build in some flexibility especially on days when long distance travel is involved.