convenient road transport from Kyoto to Tokyo

I need some advice on the transport from Kyoto to Tokyo.
Is Kodama Train of Tokaido Shinkansen is the best way? I'm looking at time and economic saving.
Thank you.

Riding the JR Kodama Shinkasen using the "Puratto Kodama" plan (this is not a ticket but a travel plan sold by JR Tokai) would be reasonably-priced and comfortable, I'd say. If you can ride an overnight but, that would be less expensive (but not too comfortable, at least for myself).

Thanks AK,
I don't quite understand what is Puratto Kodama, need your help to explain.
I am going one way from Kyoto to Tokyo only, Puratto Kodama is return ticket between 2 cities?

Puratto Kodama is a one-way tour package offered by JR Tokai Tours, a subsidiary company of JR-Central [JR Tokai].
A Puratto Kodama traveler should take one Shinkansen Kodama train among the trains designated by the vendor company JR Tokai Tours.

Personally I think Puratto Kodama is not a great deal if you care for time; I would not choose to use the slowest one among Tokaido Shinkansen super-express services only to save a cost when I can use a much faster one, under some restrictions which regular-ticket travelers do not encounter (#1).

I need some advice on the transport from Kyoto to Tokyo.
I'm looking at time and economic saving.
Is Kodama Train of Tokaido Shinkansen the best way?

I suppose not.
Your options are explained in this article.
- japan-guide.com: Kyoto: Access and Transportation
http://www.japan-guide.com/e/e2363.html

Shinkansen Kodama trains make stops at all stations on the way.
One Kodama ride from Kyoto to Shinagawa / Tokyo may last for more than 3 and a half hours.
When you travel with JR regular tickets, you can use a much faster Hikari or Nozomi service to get from Kyoto to Shinagawa / Tokyo, in which case one ride lasts for about 2 and a half hours or less.
Shinkansen Hikari trains and Nozomi trains skip some stations.
- japan-guide.com: Tokaido Shinkansen
http://www.japan-guide.com/e/e2018_tokaido.html

A Shinkansen charge is at the same price on Kodama and Hikari.
When you reserve your seat(s), a Shinkansen charge on Nozomi is a little higher by 310 yen per adult concerning a ride from Kyoto to Shinagawa / Tokyo.
When you do not reserve your seat(s), a Shinkansen charge is at the same price on Kodama, Hikari and Nozomi.

When will you travel?
Will you have an interregional JR ride to Kyoto or from Shinagawa / Tokyo within a few days? (#2)

#1:
You cannot apply for Puratto Kodama on the boarding day.
You cannot replace your Puratto Kodama plan by another plan.
A Puratto Kodama traveler should use a designated Shinkansen-only gate. (A regular-ticket traveler can use a Shinkansen-transfer gate.)
A Puratto Kodama traveler cannot get off a Shinkansen train and get on a later train on that day. (A regular-ticket traveler can do so unless he/she gets outside a Shinkansen gate.)

#2:
It is not always a fare comparison to compare the costs only looking at one JR section.
When you have a Shinkansen ride, a JR regular cost consists of a base fare + a Shinkansen charge.
In some cases, a JR base fare for a long-distance leg is lower than the total of the JR base fares for its parts.

Thanks Omotenashi for your kind advice.
my itinerary will be:
1/11 early morning transfer from Kansai Airport to Kyoto.
4 nights stay in Kyoto
5/11 Shinkansen to Tokyo
4 nights stay in Tokyo.
9/11 Fly back home from Narita.
My main purpose is
tour around Kyoto for Autumn (Arashiyama, Miyama,Tofukuji, Nara).
tour around Tokyo, Kamakura, Nikko.
I wanted to include Nagoya(Korankei) but now I cancelled the plan already.
In this case, do you think JR 7days Pass is practical for me? or just buy Nozomi/Hikari to Tokyo.
Thanks a lot

do you think JR 7days Pass is practical for me?

If you make a Nikko trip mainly by Tobu Railway, a 7-day Japan Rail Pass is not likely to pay off.
What would you visit in Nikko City?
Have you decided which area in Tokyo will you stay in?

tour around Kyoto for Autumn (Arashiyama, Miyama, Tofukuji, Nara).

Miyama? Do you mean Miyama in this article? If so, it is located in Kyoto Prefecture but outside Kyoto City.
http://www.japan-guide.com/e/e3985.html

The 3rd of November 2014 (Monday) will be a public holiday in Japan. Major tourist spots in and around Kyoto City may be crowded during the expanded weekend from the 1st to 3rd. Arashiyama area may not be in the autumn foliage season, but still the 4th of November (a normal weekday) may be better for you to visit it.

Thanks Omotenashi.

In Tokyo I will preferably stay near train station where i transfer from Kyoto. And also conveniently for me to go to Narita Airport as i do not prefer to troll my luggage on the road. Do you hv any good place to recommmend?

I stayed in Shibuya Excel Tokyu before and the airport limo bus just stop in front of the hotel lobby, but this time i am going to Narita Airport, need to find out the convenient place to stay.

In this case, do you think JR 7days Pass is practical for me? or just buy Nozomi/Hikari to Tokyo.

No, the JR Pass is unlikely to pay off for your itinerary. A Puratto Kodama ticket is a good balance between saving money and saving time. The drawbacks that Omotenashi mentioned don't really affect your itinerary, assuming you don't miss your train.

In Tokyo I will preferably stay near train station where i transfer from Kyoto. And also conveniently for me to go to Narita Airport as i do not prefer to troll my luggage on the road. Do you hv any good place to recommmend?

In that case you should book around either Shinagawa or Tokyo stations. What's your budget?

I stayed in Shibuya Excel Tokyu before and the airport limo bus just stop in front of the hotel lobby, but this time i am going to Narita Airport, need to find out the convenient place to stay

Shinagawa and Tokyo both have direct train connections to the airport.

Thanks,yllwsmrf.

I would prefer those hotel similar to Toyoko Inn with light breakfast. Though they are consider budget hotel but the room always tidy and clean. Tokyo Station is it very convenient to link to Narita Airprot?

Will it be advisable to go Mt Fuji as day trip? as i don't prefer to change hotel. Or any spot that I can have the nearer and nicer view of Fujisan.

Thanks.

There is a Toyoko Inn near JR Shinagawa station, so check that out.

As for Mt. Fuji, it depends on how much you want to see in Tokyo. You "can" do a day trip to Hakone using Odakyu Railway. But of course there is no guarantee that you get to see Mt. Fuji (simply depends on the weather). You "might" see Mt. Fuji from the JR Shinkansen from Kyoto to Tokyo.