14 days Japan: JR Rail Pass & Buses?

Hi,
We (me & hubby) will be in Japan between 25May-8Jun. We are sporty nature lovers, but since this is our first trip to Japan, we want to also see the country history & culture. So far our itinerary looks as below. I'm still reading on what we should do in Kyoto. Appreciate if I could get help on the following questions.

(1) Based on my readings I think it is still worth to get 7 days JR Rail Pass for my itinerary. Am I correct?
(2) I read in this forum to take buses from Takayama to Kamikochi, Kamakochi to Matsumoto. Can I use my 7days JR Rail Pass on these buses?
(3) However, I have a problem on 2Jun as the JR pass already invalid for the Matsumoto to Tokyo trip. To save cost, am I correct to plan to take bus for this trip back to Tokyo? Is there any other alternative that is cost effective?
(4) Is there a specific bus company that we should take for Matsumoto to Tokyo?
(5) Is our itineray looks ok?

Thank You in advance.

Itinerary
25-May(Tuesday)
Singapore to Narita arrive 2.00pm. Free&easy in Tokyo.
Night in Tokyo

26-May (Wednesday) - JR Rail Pass 1st day
Train Tokyo to Hiroshima.
Sightseeing Hiroshima & see Miyajima Torii at night.
Night in Hiroshima

27-May (Thursday):
Morning : Hiking Mt Misen & sight seeing Miyajima.
Train Hiroshima to Kyoto.
Late afternoon : sightseeing Kyoto.
Night in Kyoto

28-May (Friday)
Sightseeing Kyoto. Night in Kyoto

29-May (Saturday)
Sightseeing Kyoto. Night in Kyoto

30-May (Sunday)
Daytrip to Nara. Night in Kyoto

31-May (Monday)
Train Kyoto to Takayama.
Sightseeing Takayama. Night in Takayama

1-Jun (Tuesday)
Bus Takayama to Kamikochi. Hike Kamikochi
Night Kamikochi

2-Jun (Wednesday)
Morning : Hike Kamikochi
Bus Kamikochi to Matsumoto
Afternoon : Sightseeing Matsumoto
Bus Matsumoto to Tokyo
Night in Tokyo.

3-Jun (Thursday)
MJ exhibition, Tokyo Tower, Zojoji Temple, Roppongi. Night in Tokyo.

4-Jun (Friday)
Tsukiji market, Imperial palace/garden, Hamarikyu garden, Ginza. Night in Tokyo.

5-Jun (Saturday)
Ueno park, Asakusa, Sensoji temple, Edo Tokyo Museum, Akihabara. Night in Tokyo

6-Jun (Sunday)
Shinjuku, Meiji temple, Harajuku-Takeshita dori, Shibuya, Metropolitan building. Night in Tokyo

7-Jun (Monday)
Odaiba, Sumo-Ryogoku Kokugikan, Kabuki show?Night in Tokyo.

8-Jun (Tuesday) Flight Narita to Singapore, Depart 6.45pm

It looks like a very good itinerary to me!

Based on my readings I think it is still worth to get 7 days JR Rail Pass for my itinerary. Am I correct?

Yes, you are right.

I read in this forum to take buses from Takayama to Kamikochi, Kamakochi to Matsumoto. Can I use my 7days JR Rail Pass on these buses?

No, these buses are not covered.

However, I have a problem on 2Jun as the JR pass already invalid for the Matsumoto to Tokyo trip. To save cost, am I correct to plan to take bus for this trip back to Tokyo?

Yes.

Is there any other alternative that is cost effective?

The bus is most cost-effective.

Is there a specific bus company that we should take for Matsumoto to Tokyo?

I don't think you have a choice.

Thank you Uji for your reply. We are looking forward to our Japan trip yay!!!!