Hi there!
Here are some answers for you - I'll leave the route costs and so on as an exercise in using Hyperdia ;)
1) How much is the couchette or room? And this couchette/room can fit how many persons? Do i need to share with the rest if i'm travelling with my husband?
This depends on the type of room you choose and the train you take. The private rooms are private, so you will not have to share. Here is more information on the Hokutosei rooms and prices and on the Cassiopeia rooms and prices.
2) What is base train fare?
In Japan, fares are often itemised by use of the line, the type of train (express or normal), and the seat type. JRPass holders will not have to pay for the use of the line (basic fare), but will have to pay the other fares for Cassiopeia/Hokutosei.
3) If there are some stretch of the route that JR pass does not cover, how much do i need to pay and what are the routes?
For these sleepers it's a stretch of railway between Morioka and Aomori that is not valid JR track and will be an extra charge of between ¥3000-¥5000 each way.
4) how long is the journey if I take either of Cassiopea and Hokutosei
From station to station the journey is approximately 16.5 hours.
5) When you say it's not 100% free, this is because I have to pay for couchette or room? but the train ride is free. Am I right?
Technically yes, however you will have to pay for the express fare and also a room, as there is no standard seating on these trains.
1) So if I take this train (Akebono), do I need to pay extra for the couchettes / nobi-nobi seats? Or do i need to reserve? Have any extra charges if i need to reserve?
You certainly need to reserve, and can only do so once you are in Japan and can present your JR Pass (unless you have friends in Japan who can make the reservation for you). The actual reservation will be free (as is normal for all JR Pass holders, and if you are a JR Pass holder, the Goron to Shito seats/beds are free. Couchettes (shared compartments) and private compartments will cost extra.
1) Is the Hayabusa/Hayate shinkansen to Aomori included in the JR pass? How long is the journey from Tokyo to Aomori?
Yes, this shinkansen is 100% covered by the JR Pass. The journey time will be between 190 mins (Hayabusa) and 217 (slowest Hayate)
2) How long is the journey for Hamanasu from Aomori to Sapporo?
This journey is approx 8 hours.
1) If I would like to go to Sapporo from Kyoto, what are the trains that I can take that is included in the JR Pass? And how long will the journey be?
Here's a sample itinerary. Basic rules apply (you can use any JR bullet train except for Nozomi and Mizuho shinkansen bullets).
2) For all these trains, are they direct to the destination or do they have multiple stops along the way?
Totally depends on the route. Please check specific routes with Hyperdia.
3) What is the train that I can take from Osaka to Kyoto? And how long?
There are lots of trains from Osaka to Kyoto taking around 45mins. Please check specific routes with Hyperdia.
Hope this helps!