(A) Non-reserved is an un-assigned seat on a train. It does not mean that you will not have a seat, but you will board the un-reserved car, and find an open seat in it. In some cases, you may have to stand.
(B) I am not sure I understand your next question. I am going to assume your question in about a JR train. You will either buy a ticket, or use a pass to ride a train. If you plan to ride in a reserved car, you will use your JR Pass at a ticketing counter at the station to get a reserved ticket. The ticket, or the pass, will allow you to enter the JR area of the station, and make your way to the correct train platform. There will be departure signs at the platform that will show where the train is heading. About a minute or two before the departure time, the train will enter the station, and stop at the platform. You will then get on.
At some point after the train has departed, the conductor will enter the car, and check their list of people he/she has already checked, and go to the new passengers to check their tickets. You show your ticket, or your pass to the conductor. If you are in a reserved car, you will show your ticket and pass.
(C) I am not sure there is a "rush hour" on long distance trains. The first and last train of the day tend to be more crowded.
(D) I am not sure what a JR west pass is. I am also not sure what you mean by "save space". Do you mean a reserved seat? With a pass that covers unreserved seating, you will not have to pay the basic fare, but you will pay to upgrade to a reserved fee. I do not think that you will pay the difference between a reserved and non-reserved seat, but the full reserved seat surcharge.
(E) Many of the passes can be bought inside Japan.
(F) A five day pass is good for five calendar days. If you activate the pass at 2:00 PM, if will not expire at 2:00 PM five days later. You will just have ten hours of usage left on the first day of the pass.
I have had two times that I have really had a concern about having a seat on a train. One was the final Limited Express train from Kagoshima to Miyazaki, and another was a Shinkansen from Hiroshima to Osaka during Golden Week. This was on a trip where I purchased a Green (first class) JR Pass. On the trip form Kagoshima to Miyazaki, the first class car was full, and I have never been on a train where the first class car was full. My guess is that all reserved and un-reserved seats were sold, and people had to purchase first class seats to get home. On the trip during Golden week, there were still seats in first class, but I saw row upon row of high school students on the platform waiting to get on a train. You are not traveling during Golden Week , and should not have to worry about students on a field trip.
One of the reasons I get a first class (green) pass, is to ride the wide-view Limited Express trains in the first car, which is a first class car. On a wide view Limited Express, there is a glass panel between the first class seats and the Engineer's Compartment. You can see out the front of the train. My first experience with this was going from Okayama to Takayama on a Marine Liner.
https://en.wikipedia.org/wiki/Marine_LinerOn the Marine Liner, here is a row or two of first class seats just behind the Engineer's compartment. There are U-Tube video's of the ride. If you do get a first class pass, try to reserve the right-most seat in the front row. I have heard that one of the most scenic train rides is from Nagoya to Takayama on the wide view Hida.
http://toretabi.com/train/central/train_02/index.htmlIf you are worried about getting reserved seats, then I would advise you to get the 7 day JR Pass, which allows you to get reserve seats. I would then think about going to Takayama from Kyoto, and doing Kanazawa from Takayama.
It depends on how much of a train buff you are.
