you can reserve seats on Shinkansen now BEFORE you have exchanged your Pass.

It is on JR East website - link to the reservation site. You still need to join and provide your CC No. but once you get to Japan and pick up your tickets, show them your JR Pass (You can do both exchange and pick up tickets at the same place), they will take care of that.

You can only reserve Shinkansen seats online now. All other trains reservations must be done at the "green window".

The Cherry Blossom comes early this year due to exceptional warm weather in February.

Flowers start to bloom on March 20 in Tokyo per weather forecast. during Cherry Blossom period (about 10days) travel between Tokyo, Kyoto and Osaka could be heavy. And of course the golden week in Japan.

I would avoid golden week to visit Japan by all means.