23 Aug (Thu) - depart Denver
24 Aug (Fri) - arrive Narita, night in Uguisudani
25 Aug (Sat) - Tokyo, recover from jetlag, second night in Uguisudani
26 Aug (Sun) - go to Fuji-Yoshida, explore Fuji-go-ko, Fire Festival, night in Fuji-Yoshida
27 Aug (Mon) - climb Fuji (probably the lazy way, from 5th station), overnight in hut at 8th Station
28 Aug (Tue) - watch sunrise, descend, go to Yokohama, de-facto first night at WorldCon
-- WorldCon --
04 Sep (Tue) - exchange JR Pass in Yokohama, train to Hakodate, night in Hakodate.
05 Sep (Wed) - explore Hakodate, train to Sapporo, explore Sapporo, night in Sapporo.
06 Sep (Thu) - train to Asahikawa, explore Asahikawa, continue to Bihoro, night in Bihoro
07 Sep (Fri) - explore northeastern Hokkaidou, perhaps Shiretoko, second night in Bihoro
08 Sep (Sat) - more exploration, last night in Bihoro
09 Sep (Sun) - afternoon train back to Hakodate, night in Hakodate
10 Sep (Mon) - train back to Tokyo, night in Uguisudani
11 Sep (Tue) - depart Narita, arrive Denver
This is probably pretty close to the final plan (most reservations have been made, but not quite all, thanks to the two-month window). The schedule should be loose enough that none of the trains should be too bad (the longest in terms of distance is Yokohama to Hakodate, at almost 1000km, but the longest in terms of time would be Bihoro to Hakodate, at a bit over eight hours, slightly longer than Yokohama to Hakodate). Bihoro to Tokyo is just barely possible, but would take fifteen hours and have several ten minute connections -- cutting that down to two days with a night in Hakodate is better.