OP,

JR Pass cannot be used for Nozomi, but can be used on all other Shinkansen trains. A 7-day JR Pass would be the way to go if you opt to use NRT and Shinkansen. You must purchase it OUTSIDE Japan and then exchange the voucher at JR station at NRT (or any major JR Station.)

Depends on what time of the year you are going, there is generally No Need to buy the First Class Pass, and No Need to make advance reservation for the Shinkansen rides. Besides, you dont want to go to Japan during their "Golden Weeks" Annual National Vacation time anyway. Golden Weeks are not the same weeks each year, but they fall in May.

Just buy the Ordinary Class Pass, the train seats are better than your domestic first class seats with much more legrooms. In some cars there are even tables in between rows - the seats can turn around to face each other.
In fact, watching the cleaning crews (usually women team) do their cleaning and turning around the seats at the major stations during the few minutes time of the stops, are quite a scene to show the high efficiency of Japanese operation.

The Platform is clearly marked for boarding area by the car number. The "Free Seat" section usually start from the 3rd or 4th car if I remember correctly. Usually there would be some Japanese already lining up there, so you can just follow them.

If in a rush, you can always hop on the train and walk to the "Free Seat" section - the "Free Seat" means No Advance Seat Assignment Seats. In Japan, the word Free does not mean the samething as here. If it is no charge, then they use "No Charge", not "Free".

If you are stuck at the smoking section at boarding, walk to the nonsmoking section and usually you can find seats at the next stop.