How to purchase Japan train tickets online and also Japan scenic itinerary?

For travelling outside eastern Japan, there is no way to buy or reserve tickets from abroad. (Unless you can read Japanese)

For eastern Japan, you can reserve train tickets on the JR EAST network via their website (found here).

NOTE: JR EAST only covers the following part of Japan:

Even if you can't reserve a train ticket in advance, you will find that unless you are travelling during one of the three busy periods, you will have no trouble finding a seat without reserving it in advance. Simply show up to the counter, buy a ticket (or show your JR pass) and the attendant will hand you a seat reservation.

The busy periods include:

• Golden Week: usually around 28 April to 7 May
• Obon: Usually 10 August to 20 August
• Shogatsu: 28 December to 4 January

As blackbird57 and Federico mentioned, if you plan on travelling by rail, a JR pass can be extremely worth it. Use websites like Hyperdia to get a rough estimate of the total cost of your train tickets and compare that to the cost of a JR pass, you could save lots of money.

Source

You can't buy individual tickets beforehand online.

If you're thinking about getting a JR pass, you need to buy an exchange order from an approved reseller or travel agency in your country before arriving in Japan and then exchanging it for an actual pass once you arrive.

The pass then becomes your ticket on JR networks (high speed trains and some lines within cities). There's a very informative article on Japan Guide about this.

If you don't want to buy a whole pass, you can still buy individual tickets but only in Japan. Most stations have machines where you can buy it yourself

1. Is there any official Japanese website to buy train ticket online?

I assume you're speaking about the Train ticket discount for foreign tourists.

No: http://www.japanrailpass.net/en/purchase.html

Buy your Exchange Order for the JAPAN RAIL PASS at one of the following sales offices or agents before coming to Japan. JTB Corp., Nippon Travel Agency, KINTETSU INTERNATIONAL, Tobu Top Tours, Japan Airlines, All Nippon Airways, JALPAK, and their associated agencies.

There are websites that sell the JRP, but they are not official outlets.

All the official points of sale are listed in the page linked, divided by geographical region.

I skipped the rail pass since a 2 week pass ended up being more than the journeys we needed. (Tokyo,Kyoto,Odawara,Tokyo)

The JR vending machines take Mastercard so just bought the tickets when needed. FYI the Subway machines didnt accept foreign cards.

If you have time, 1 full day in Hakone was amazing. Spent 3 nights in Kyoto, wish we did more.