Hi,
Japan Rail Pass is very much worth it if you are traveling that far as you can also use it on local JR lines etc.
Using a wheelchair, you will still need to make reservations for the Shinkansen to get the accessible seat with or without the JR Pass. When you have decided on the train you want to ride on, go to a “Midori no Madoguchi” (found at most larger JR stations) and talk to the staff. If you don’t have the pass, you will need to buy the tickets. If you have the pass, they will book the seat and give you a ticket for the reserved seat (to show it is reserved by you). Either way, you need to make the reservation in person. Note it can take them a while to confirm accessible seat availability etc, so be sure to leave an hour or so open. (They are getting better now…)
It has been 15 years since I used the pass (I live here and cannot get one anymore), but I think the pass covered the entire cost. If not the full cost, it covered the boarding cost and you may need to pay a tad extra for the reserved seat.*
*You actually get two tickets per person if you get a reserved seat. One covering the ride (and sitting in an unreserved seat if available), and then one for your reserved seat (showing the seat number). The reservation ticket is needed if you want the accessible seat.