Itinerary comments

Have already bought JR 14 day pass and plan t use Suica/NEx for intial trip into Tokyo
itinerary at this point is
16/9 Arrive Narita 17.35. Transfer to hotel in Ebisu
17/9 Kanto Eartquake Memorial and Ebisu Brewery
18/9 Tsukiji markets; Hanarikyu Garden, Sumida cruise to Asakusa
19/9 Nihon open air museum in Kawasaki. Overnight Ebisu
20/9 Train to Nagoya then visit Inuyama. Overnight Nagoya. Leave ost of luggage
21/9 Train to Takayama. Stay in ryokan
22/9 Bus to Shinagawa. O'night in Takayama
23/9 Back to Nagoya. Visit castle and museum
24/9 Train to Kyoto stay near Gion/Higashiyama. Visit Kiyomizo Temple and Pottery Street
25/9 Ginkakuji, Philosophers Walk, Heian Shrine then Teramachi and maybe Nijo Castle
26/9 Possibly day trip to Himeji O'night Kyoto
27/9 Golden Pavilion. Afternoon train to Osaka. Visit Umeda Sky Building
28/9 Osaka Castle, Museum and Muramon MarketO'night Osaka
29/9 Morning visit to Nara. Visit Fushimi Inari Shrine in afternoon. O'night Osaka
30/9 Train back to Narita from Osaka via Tokyo for flight at 19.00

Too much? Not enough? Have been to Tokyo before and done Ueno/Edo Museum/Meiji shrine etc.

26/9

On 20/9, you could consider visiting Inuyama along your way from Tokyo and Takayama and end the day in Takayama rather than returning to Nagoya, if the luggage situation allows.

On 22/9 I assume you mean Shirakawago rather than Shinagawa.

Instead of going Nagoya - Takayama - Shirakawago - Takayama - Nagoya - Kyoto, I resommend to travel as follows, although I realize that this more efficient route could cause luggage complications:

Nagoya - Takayama - Shirakawago - (via Kanazawa) - Kyoto

Lastly, I recommend to visit Fushimi Inari Shrine during your days in Kyoto, as the shrine is located in central Kyoto. Visiting it in combination with Nara from Osaka would require a major detour.