Tokyo-Hakone-Kyoto-Osaka

Hi All

I would like to ask based on below accommodation plans, how would you recommend on the passes (JR Pass/Hakone Pass/Fuji Hakone Pass) available for tourist? We will be travelling on 27 April 2017 with 2 large luggages.

Tokyo: 2 nights (Nearest Station: Shinjuku Sanchome Station)
Like to visit: Shibuya, Shinjuku, Ginza, Ashikaga Flower Park, Tsukiji market

Hakone: 1 night (Nearest Bus Stop: Ohiradai)
Like to visit: Fiji Shibazakura Festival, Lake Ashi, Hakone Ropeway, pirate ship. (Shrine and Gotemba Premium Outlet, Onsen optional if time cannot fit.) Or we can use 2 days here after checking out from Hakone?

Kyoto: 2 nights (Nearest Station: Kyoto Shiyakusho-mae Station)
Like to visit: Temples, Gion

Osaka: 4 nights (Nearest Station: Daikokucho/Namba Station)
Like to visit: USJ, owl cafe, USJ Shinsaibashi, Dotonburi, Amerikamura, Umeda.

Biggest Woes: How do I best fit Shinjuku-Hakone-Fiji Shiba Sakura Festival-Kyoto with the luggage in mind?

Thanks!

Japan Rail Pass: Forget it. This is for multiple long distance Shinkansen trips.

27 April 2017 was posted on 2017/4/26? Now in Osaka?

Tokyo: 2 nights could be either 2N3D, 2D2N, or 1D2N.
2N3D: D1: Shibuya, D2: Ashikaga Flower Park, Shinjuku, D3: Tsukiji Market, Ginza
2D2N: D1: Ashikaga Flower Park, Shinjuku, D2: Tsukiji market, Ginza, Shibuya
1D2N: N1: Shibuya, D2: Tsukiji market, Ginza, Ashikaga Flower Park, Shinjuku (tough)
Ashikaga Flower Park mainly by Tobu, such as 1650 yen for Shinjuku3Chome 0503-(Toei Shinjuku)-BakuroYokoyama/HigashiNihonbashi-(Toei Asakusa)-Asakusa-(Tobu)-MinamiKurihashi-(Tobu)-Tochigi-(JR Ryomo)-Tomita-0805 Ashikaga Flower Park. Others by JR, subways, and bus, depending on the pace. Buses could be OK for the 2N3D case.

Hakone: Fuji Shibazakura Festival is on the west side of Mt Fuji, while Hakone on the east side. Shibazakura belongs to another destination, Kawaguchiko. The order might be Hakone Ropeway, Lake Ashi/Pirate ship, Shrine, Gotemba Premium Outlet (at evening), and Onsen (at night). Gotemba is far, drop?

Osaka:
USJ, one full day.
owl cafe, and Umeda
Amerikamura, Shinsaibashi, and Dotonburi
So, 3D4N?

Biggest Woes
1: Shinjuku - Hakone is easy; 1670 yen for Shinjuku3Chome 0523-(TokyoMetro Shinjuku)-ShinsenShinjuku/Shinjuku-(Odakyu)-Odawara-(Hakone Tozan Bus Togendai)-Ohiradai 0733.
2: Shibazakura on the way to Kyoto. Ohiradai 0827-(Bus)-Odawara-(JR Kodama 639)-ShinFuji 0945-(Fujikyu Bus)-1100 Fuji Shibazakura Festival 1330-(Shibazakura Liner)-1445 ShinFuji 1511-(JR Kodama)-1734 Kyoto-(Kyoto City Bus)-1801 KyotoShiyakushoMae
Shibazakura Liner on Saturdays, Sundays, and Holidays only. http://www.shibazakura.jp/liner/
Coin lockers are near South Exit at ShinFuji station. https://www.jr-odekake.net/eki/premises.php?id=0520151

KyotoShiyakushoMae 0541 -(Subway)-KeihanYamashina/Yamashina-(JR)-Osaka/Umeda-Daikokucho 0710
ImamiyaEbisu 0500-(Nankai)-0558 KIX
Adjust the departing times with Google Maps.

Hakone Free Pass is 2 or 3 days. http://www.japan-guide.com/e/e2358_008.html
Fuji Hakone Pass is 3 days. http://www.japan-guide.com/e/e2358_014.html
If you steal night(s) from Osaka, then consider Fuji Hakone Pass to go around Kawaguchiko as well. Hakone Free Pass for 2 days could be your choice if you start from Shinjuku quite early. Daytime is from 0454 to 1824 on Apr 27 at Tokyo.