Ideas for itinerary?

I'm going to Japan on the 12th April for 7 days and staying in Shinjuku. I've been once before and been to quite a few places in Tokyo, Kyoto and Hiroshima.

Some places I want to see this time are:

Tokyo:

Shinjuku Gyoen
St Mary's Cathedral, Bunkyo
Yoyogi Park, Harajuku
Roppongi Hills
Ginza, Chuo
Meiji Jingu, Harajuku

Kyoto:

Kiyomizu-dera Temple
Fushimi Inari-taisha
Philosopher's Walk

I saw that Ginkaku-ji is being renovated, is it not worth visiting now or is their a garden worth walking around?

Would it be too much to add Osaka in on the same day if I'm not staying over in Kyoto?

Does anyone have any other ideas of cool things to see that I might be forgetting?

Also I just checked and the JR pass now seems to be £208 and last year I paid about £120... is this correct?

I saw that Ginkaku-ji is being renovated, is it not worth visiting now or is their a garden worth walking around?

The garden is still worth seeing. But considering that the main building is under construction, I would give various other sights a higher priority.

Would it be too much to add Osaka in on the same day if I'm not staying over in Kyoto?

Add to what? Ginkakuji?

Also I just checked and the JR pass now seems to be ��208 and last year I paid about ��120... is this correct?

The cost remains at 28,300 yen. However exchange rates have changed quite drastically - not in the favor of the British pound:
http://www.japan-guide.com/e/e2196.html

Thanks, I might miss it out then.

Sorry I meant would it be too much to do the things in Kyoto and then go onto Osaka in one day?

Ahhh OK, I didn't realise it was going to be affected so much!

It is no problem to go to Osaka in the evening. The two cities are only 30 train minutes apart from each other:
http://www.japan-guide.com/e/e4006.html?aFROM=2157_2158