Hakata-Kansai-Tokyo Transport and Places

From my research, the JR Pass is more covered online but does not meet my needs.

9-Feb Fri HND Tokyo Haneda - KOJ Kagoshima Airport
25-Mar Sun KOJ - Fukuoka Airport
5-Apr Thu Fukuoka Hakata morning - Hiroshima - Miyajima island - Takamatsu late afternoon
6-Apr Fri Takamatsu - Sannomiya Station, Kobe
7-Apr Sat Sannomiya Station, Kobe - Kyoto
19-Apr Thu Kyoto - Osaka
25-Apr Wed KIX Osaka Kansai Airport - HND

I inquired JR West about booking the Sanyo San'in Area Pass online after arriving in Japan due to the booking limit of 1 month in advance that I would exceed. I could but they recommend booking before arriving in Japan because you can reserve up to 6 trains for the Shinkansen and the Ltd. Express HARUKA through their website and that it is possible that they are unable to book your desired trains during the high season.

A very useful resource is the jprail blog website.

Now my questions:
Transportation
What is needed to make online seat reservations from at most 27 days prior? Could the booking confirmation email be sufficient?
Ekiren: around what time to rent a bicycle successfully?

What Pass to use for an extended time in Kyoto and Osaka only? Or an IC card?
How to use JR West Sanyo San'in Area Pass, Kansai Thru Pass, IC card and Tokyo Subway Ticket in more details;
tickets purchase (use the Pass/IC as ticket or buy ticket with it?),
at the gates; departure and arrival,
on the train,
How do you know when to use the "Fare Adjustment" machine, that is when the fare was paid incorrectly?
Whom and how to properly ask for help at the station?
Do I need Advance Booking for peak season with my schedule?

Fly rather than train for long distance?

What to visit in
Hakata (is the FUKUOKA TOURIST CITY PASS good?),
Hiroshima (maybe use the meipurupu bus tour?) and Miyajima in less than 3 hrs each,
in 1/2 a day in Takamatsu,
in Sannomiya, Kobe in 1/2 a day,
and around Naniwa ward in Osaka?

Thank you very much
Happy year end

Too many questions. So confising. Hopefully someone can understand and answer them.

As for you 5th of April day. That is not really realistic. You have 5 hours of travel. And you are attempting to see Hiroshima and Miyajima in one day, and attempt to store baggage somewhere also. I'd do an overnight stay in Hiroshima.

Your post raises a number of questions, actually.
So you are flying down to Kagoshima for over 6 weeks? Why?
I've traveled the same routes you did, around the same time. Never had any problems getting a seat at all.
So you may be blowing your whole thing out of proportion. You also might look at getting the JR Setouchi Area Pass instead - it's a bit cheaper though seating is all unreserved. And if you are trying the chase the cherry blossoms, you also might consider a few other places. Iwakuni was absolutely delightful in cherry blossom season, and the mountaintop castle gave an excellent view over the whole area.
https://youtu.be/0COOZXi66mM

Also your idea of seeing Hiroshima and Miyajima in half a day or so is just not realistic. Both together will easily fill up a whole day. Miyajima also has a number of great places for cherry blossoms, and is not a place you want to rush through.
https://goo.gl/fAz4ax
If you get lucky, you can see Miyajima both at high tide (when the shrine looks better) and low tide, where you can walk on the beach up to the giant torii gate.
You could also spend a full day in Takamatsu - it is one of the more interesting cities on Shikoku. The Ritsurin Garden is a must-see place.
https://youtu.be/afx-Ju52FiY
And Yashima + Shikoku Mura are worthwhile too.
https://youtu.be/EQgQ9V3qk38
I would stick with the IC cards in Kansai, unless you travel long distance like a day trip to Himeji. In Tokyo, the 2-3 day subway pass can save some money.
http://www.tokyometro.jp/en/ticket/value/travel/index.html#anc03
In Fukuoka the Tourist Pass is good if you think you'll also be taking the bus. But many good sights are close to a subway station, so a subway day pass might suffice very well. As for what to see, try looking through:
http://www.thejapanfaq.com/fukpic.html
One place you should not miss is the Nanzoin Temple just outside the city. There is also one of the nicest cherry blossom spots along the way, Kayoichi Park, in Kasuya. And almost unknown to everyone.
https://youtu.be/pYKNmvevAC4
Inside Fukuoka, two excellent blossom places are Maizuru Koen and Nishi Koen, both near Ohori Koen, so very convenient.
http://bit.ly/1KAm8cU
The airport in Fukuoka is very conveniently located, but in other cities are far less so - rail would be the ideal way to travel.

Thanks Ken for your help. I appreciate it.

I am staying in Kagoshima for 6 weeks to enjoy nature and for the climate.

My issue is that no pass is sold in my country and most of my train trips would be after more than a month in Japan. So I cannot book online before arriving in Japan and planned to do it after.

Reserved seats on trains can be booked one month out from the day you wanna travel. So you have plenty of time to organize and book tickets when staying in Kagoshima for six weeks.