Ltd. Exp Kaiji - reservation

Hi, I'm planning to take the following route from Kyoto coming July: https://i.imgur.com/KEe4fJl.png

I noted that the Limited Express Kaiji is reservation-only, so I'd have to buy a ticket in advance. Should I miss the Limited Express due to a delay on the Shinkansen or the Yokohama Line, am I entitled to get a refund for my Limited Express ticket? Could I exchange the Kaiji ticket for a ticket for the next Ltd. Exp Azusa instead or could I use the ticket to take the Chuo Line between Hachioji and Otsuki and get a refund for the Limited Express supplement?

One more thing, is it sufficient for me to buy just a Limited Express ticket and use my Suica card to pay the base fare from Yokohama to Otsuki?

Why not get off the shinkansen at Mishima station and get the bus to Kawaguchiko? Cheaper and quicker...

Because I'm going to Fujiyoshida, not to Kawaguchiko?

Hmmm I would say it depends on where in the Fuji-Yoshida you are trying to get to? The bus does have a stop near Fuji Q Highland which puts it near some hotels in Fuji Yoshida like the West Inn Fuji Yoshida. The drop off point is only about 2 kms from the Fujisan Station Hotel if that is your destination.

Good luck!

I'm going to Fujiyshida Sengen Shrine.

Fujiyshida Sengen Shrine is not far from Kawaguichiko or even far from the Mt Fuji station, so the bus from Mishima isn't a silly option.

I will add a few extra observations:
- transfer at Shin-Yokohama will take about ten minutes for a first timer with luggage - not especially hard, but it is between two quite separate platforms.
- Hachioji also isn't a hard transfer - seven minutes is ok, but you don't have a lot of time. Be prepared to carry luggage up stairs (there are some escalators/lifts).
- your refund if you missed your Kaiji is only 750 yen. If JR cause you to miss the train due to a delay, then you would be entitled to a refund. If you miss a train for some other reason, it depends (there are some complex rules and I'm not inclined to delve into them this morning).
- using suica - given you enter the rail system in Kyoto, you could get the express ticket and do a fare adjustment at Otsuki, but there is no reason why you wouldn't get the base fare ticket Shin-Yokohama to Otsuki when you get your other tickets.

Thanks for your observations. I'll be using my Suica linked to the smartEX App to use the Shinkansen. The plan is to then use the Suica for the traject from Shin-Yokohama to Otsuki. I prefer using Suica instead of buying separate tickets (which could be lost, etc.) whenever possible.

1), 2)
No problem, you can.

3)
JR "base fare" ticket (not including LtdExp ticket) is cheaper if you use a long distance.
I does not calculate whether it becomes cheaper by adding S-EX and left section's fr Shin-Yokohama.

Smart-EX can not be used for left section, nor can it be used only for LtdExp ticket of Shinkansen.

You can use Suica btw Shin-Yokohama stn and Fujisan stn via Otsuki, but no big discount.
The left section's base fare ticket price fr Shin-Yokohama to Otsuki via Otsuki is same
even if you get on the JR line via Yokohama Line or via Shinjuku stn(LtdExp Azusa and more).
The amount of money for LtdExp tickets change in the section where you get on.

4)
The reason for recommending the shortcut in the above is that it is roundabout fr Shin-Yokohama.
You look at the map but if can not find the timetable, it may be difficult to understand in short time.
https://goo.gl/maps/6hwtuEAQPvYPNSPSA
https://goo.gl/maps/45qLnjcbnFK5nWd79
(note)
Shinkansen Nozomi doesn't stop at Mishima stn, and HyperDia is not covered this bus.
http://bus-en.fujikyu.co.jp/highway/detail/id/29/#routemap
There is express bus to Kawaguchiko stn fr near Kyoto stn and even fr near Nagoya stn, though.
http://bus-en.fujikyu.co.jp/highway/

I was planning to use S-EX for the entire Shinkansen fee from Kyoto to Yokohama, both the base fare and the Ltd Exp fee. I don't understand what you mean by 'left section'.

I'd use my Suica for the base fare from Shin-Yokohama to Otsuki and just buy a separate ticket for the Ltd Exp Kaiji from Hachioji to Otsuki.

To arrive at Mishima Station before 10.10, I'd have to take the Shinkansen in Kyoto at 7.56, which is earlier then if I'd do the entire journey by train. The next bus from Mishima to Kawaguchiko doesn't depart until 12.10. The Express Bus from Kyoto to Fujiyoshida goes overnight, which wouldn't allow me a good night of rest.

That "left" is not the meaning of direction (opposite of the right), "remaining".
https://en.oxforddictionaries.com/thesaurus/remaining
= fr Shin-Yokohama to Fujisan via Otsuki stn.

And, Suica also vaild for FujiQ rail stns.
http://e.fujikyu-railway.jp/column/ic_card.php

Yes, I indeed meant to use it for the Fujikyu Railway too.

And while you need to leave on a train 16 minutes earlier to make the 10:10 bus at Mishima, you arrive at Kawaguchiko or Fuji Q Highland Park at 11:45 or 11:35 respectively which is a lot earlier than the 12:24 you arrive at Fujisan station.

I get 13770 yen to Fuji Q Highland/Kawaguchiko vs. 15670 on your original plan. The shrine is a 30 minute walk from Fujisan Station or you can take the bus but unless you are planning to walk, you can also take the bus from Kawaguchiko Station (it takes all of 10 minutes longer) or you can use the 1900 yen you didn't spend on the other route to take a taxi from Fuji Q Highland to the shrine, as it is 2.5 kms from the Fuji Q Highland. So if you took the 10:10 you could be at the park at 11:35 and catch a taxi and be at the shrine by 11:45, 25 minutes before your original train even arrives at Fujisan Station.

So while you leave 16 minutes earlier, you will reach your final destination of the shrine more than 16 minutes earlier and you will have fewer transfer where something could go wrong.

Good luck!

I will see what to do, thanks for all of your input!