Comfort and food
I have taken this train several times after arriving from the US and if you're an adventurous traveler, it's not so bad. Take it for what it is --- a great new adventure in another part of the world. Especially if it is your first time in Japan, don't be in such a hurry to make a fast connection. Tokyo Station, while daunting to some, is a paradise for people-watchers so give yourself ample time to both navigate between trains and take-in the view.
Don't forget about the food - just walking through Tokyo Station is a culinary adventure so give yourself time to look at all the food stalls - and stop to buy a snack or 2 for the train (less expensive and better selection than the cart that goes up and down the aisles on-board.)
One last suggestion - and a well-deserved treat after that long flight - for not too much more money, if you can afford it. I recommend riding in the Green Cars. It's the 1st class equivalent (without the extra service) with much wider seats (2&2 vs. 3&3 in Regular cars) and more peace and quiet.
Whatever you do - enjoy the ride - and I hope you get a clear and sunny day for the beautiful view of Mt Fuji out the right-side windows.