Hi there,
Because you will be making extensive use of the Shinkansen bullet trains, I would suggest purchasing the JR Pass for your itinerary, but please be aware that you will need to purchase the ferry ticket from either Uno or Takamatsu port separately - the JR Pass will take you to either via local trains from Okayama, but the ticket is not included. However, the cost of the ferry ticket is relatively inexpensive compared to the cost of rail travel so it shouldn't be a big problem and either way you'd have to purchase separately.
For the first part of your question, I'm afraid I'm not quite sure what you mean - Tokyo to Sapporo does not have the option to travel via Ltd Express train, only Shinkansen because of the distance between them. Perhaps you've encountered a Japanese website with a poor translation, and the 'fare ticket' refers to the price of the Shinkansen ticket?
Kind regards,
Alexis