Checking train fares on www.hyperdia.com shows that you would benefit from buying a 14-day ordinary JR Pass. You can buy a SUICA card and use for the Tokyo Metro and yes you should buy a day bus pass for Kyoto if you plan on utilizing the bus option throughout Kyoto. Personally I do not like using buses in Kyoto as they are always so crowded but I do use them once in a while....
You can find a lot of useful information about Japan using this site:
http://www.japan-guide.com/

Like this very helpful page on getting around on a train in Japan

http://www.japan-guide.com/e/e2016.html

or this page which explains transport within Tokyo

http://www.japan-guide.com/e/e2017.html

Or how to purchase and use your SUICA card

http://www.japan-guide.com/e/e2359_002.html

Lots of information here so check it out then come back with more questions.

Aloha!

Toyama to Narita by JR is a 5-hour trip, so I took a look at the option of flying, but flying Toyama to Narita Airport is not a great option.

The idea was a 7-day pass for May 2-9 and then flying out of Toyama (using 5,000 United miles for the one-way). But neither ANA nor JAL fly to Narita. ANA does fly from Toyama to Tokyo Haneda Airport. That would be an option if you wanted to spend the last night in Tokyo. Otherwise, you would still have to travel from Haneda to Narita.

But, the 14-day fits your plan.

... flying Toyama to Narita Airport is not an great option.

and, of course, May 2-9 would be EIGHT days, so nevermind.