The new itinerary looks better, but I would think the transition from Koya to Nara to Hiroshima is a bit rushed.
Especially since near Hiroshima is Miyajima island (the ferry to it is covered by JR pass), which deserves half a day itself.
I think the place you can free up time is by arranging Hakone and Fuji Five lakes off the JR pass. The reason I'm saying this is that though the places are expensive to get to, the JR pass doesn't offer you great savings in transport.
For example, here's a budget by using the JR pass:
You get to Odawara from Tokyo: free.
From Odawara you can purchase a Hakone free pass for 2 days: 3900 Y
This takes you around the Hakone loop and gets you to Gotemba the next day.
As Uji mentioned, you then catch a bus to say Kawaguchiko: 1470 Y
From Kawaguchiko to Otsuki by train: 1100 Y (Fujikyu private line to Otsuki)
Otsuki to Tokyo: free
Total: 6470 Y (and the connections are more complicated)
If you did this off JR pass:
From Shinjuku to Hakone via Hakone Free pass: 5000 Y (for 2 days)
Bus from Gotemba to Kawaguchi ko: 1470 Y
Bus from Kawaguchiko to Tokyo: 1700 Y
Total: 8170
You can check the URLs here for the passes and access:
http://www.japan-guide.com/e/e5206.html?aFROM=5200_6900http://www.japan-guide.com/e/e2358_008.htmlhttp://www.japan-guide.com/e/e6905.htmlBasically for 1700 Y more, you can use those two days you have allocated on the JR pass to free up some time in western Japan so you have a better time, and also include Nikko at the end of the trip, which is an expensive day trip that would otherwise be entirely covered by JR pass. And for your last day you can use the Narita express (assuming your times work out), which is a comfortable and quick way to get to the airport from central Tokyo.
I might suggest a revised schedule like this:
18/09/2011 Tokyo
19/09/2011 Tokyo
20/09/2011 Yokohama day trip
21/09/2011 Kamakura day trip
22/09/2011 Hakone overnight (Hakone free pass)
23/09/2011 Fuji 5 lakes over night
24/09/2011 Fuji 5 lakes to Tokyo (bus)
25/09/2011 Tokyo to Takayama (Day 1 of JR pass)
26/09/2011 Takayama to Kanazawa noon-ish
27/09/2011 Kanazawa all day; pm train to kyoto
28/09/2011 kyoto
29/09/2011 kyoto
30/09/2011 kyoto
01/10/2011 mt koya overnight
02/10/2011 mt koya Am to Nara pm
03/10/2011 nara AM; then to hiroshima
04/10/2011 Hiroshima and Miyajima
05/10/2011 Hiroshima to Tokyo
06/10/2011 Nikko
07/10/2011 tokyo
08/10/2011 depart (use JR pass last day to get to Airport via Narita express)
Finally, as for hotels, it's perfectly fine to leave luggage there and pick it up later that day. Most places either have a dedicated luggage room or will bung it in their office (i.e. if it's a minshuku or small ryokan).
Good travels.
mike