Itinerary for Tokyo-Osaka-Kyoto-Hiroshima

Initially we're going to Japan for 7 days at the end of this august, and planning to go to Tokyo-Osaka-Kyoto, but on the last minutes decide to extend the trip and put Hiroshima on the list. So the itinerary will be:
Day1: arrive in Tokyo and city sightseeing on the night
Day2: Osaka trip, stay in Osaka
Day3&4: Kyoto trip, stay in Kyoto
Day5: Nara & Iga Ueno trip, planning to stay in Nara
Day6&7: Hiroshima&Miyajima trip, stay in Hiroshima
Day8: Going back to Tokyo, drop in in Nagoya along the way
Day9&10: Tokyo tour,
Day11:going back to our country
We're planning to use JR pass on our day 2 to day 8.
What we like to know is do JR pass cover the transportation inside the city of Osaka and Kyoto?
Any advice on getting around in Kyoto? We're planning to visit Kyomizudera, Higashiyama, Gion, kinkakuji, Fushimi Inari Shrine, Sanjusangendo and Nijo Castle, will it be enough to go to those places on 2 days?
Will it be convenient to go to those places by bycycle?

And we're going to travel with a friend who has "student visa", is it means that our friend ineligible for purchasing JR pass? If our friend ineligible for JR pass, any advice so that our friend could travel with us but still economically sound? Any pass our friend could use on the JR line?

I appreciate all the help and input!

Day1: arrive in Tokyo and city sightseeing on the night

Which airport do you land at? At what time? Where did you plan on staying in Tokyo?

If you arrive at Narita consider Suica + NEX return Package
http://www.japan-guide.com/e/e2359_002.html

Day2: Osaka trip, stay in Osaka
Day3&4: Kyoto trip, stay in Kyoto
Day5: Nara & Iga Ueno trip, planning to stay in Nara

If you wish you could use one (or two) places as a base instead of switching hotels so much. I would probably overnight in Kyoto from Day 2-5. Nara/Osaka are less than 30 minutes from Kyoto.

Day6&7: Hiroshima&Miyajima trip, stay in Hiroshima

Seems fine.

Day8: Going back to Tokyo, drop in in Nagoya along the way
Day9&10: Tokyo tour,
Day11:going back to our country

Seems good.

We're planning to use JR pass on our day 2 to day 8.

Sounds good.

What we like to know is do JR pass cover the transportation inside the city of Osaka and Kyoto?

Kyoto, JR is basically useless. Probably consider the One Day Bus Pass (500 yen).

In Osaka JR Pass is not that useful, so just pay for individual tickets depending on where you need to go. Should be relatively cheap.

Any advice on getting around in Kyoto?

Bus or Subway, and walking

We're planning to visit Kyomizudera, Higashiyama, Gion, kinkakuji, Fushimi Inari Shrine, Sanjusangendo and Nijo Castle, will it be enough to go to those places on 2 days?

Yes, if you don't mind a fast pace.

Will it be convenient to go to those places by bycycle?

No.

And we're going to travel with a friend who has "student visa", is it means that our friend ineligible for purchasing JR pass?

Correct, they cannot get a JR Pass

If our friend ineligible for JR pass, any advice so that our friend could travel with us but still economically sound?

There are some student discounts available for Shinkansen, read this thread:-
http://www.japan-guide.com/forum/quereadisplay.html?0+93717

In general JR tickets will still be relatively expensive.

If the student is on a budget perhaps they could take overnight buses and meet you at the destination, even if only for some of the trip.
http://www.japan-guide.com/e/e2366.html
http://www.japan-guide.com/e/e2369.html

Any pass our friend could use on the JR line?

No.

Enjoy your trip!

Hi GC3, thank you for your input.
We're landing at Haneda airport, so basically we're unable to use Suica+NEX package. We will be staying somewhere near Gyotoku station, so probably we will be taking Keisei Bus from Haneda. Any suggestion beside taking the bus?

For Gyotoku there are some train options from Haneda. Just use Hyperdia to show them:-
http://www.hyperdia.com/

Having said that the trains won't be much cheaper than the bus and the bus will be more convenient assuming you land at a time close to the bus schedule!