Help with 2 day visit to Hakone

We are planning to visit Hakone on Nov. 22 (Sunday) and Nov. 23 (Monday). Since we already have confirmed accommodations in Tokyo, we plan to use our JR Pass on both days to Hakone. Would appreciate help in suggesting best itinerary to cover the places we are interested in seeing and experiencing, given we are traveling on a Sunday/Monday.
The following areas we wish to cover:

Gora area--Odawara Castle, Koen, Visit Crafthouse and do glass blowing

Owakudani, Venetian Glass Museum, boat ride on Lake Ashi, ride Hakone ropeway and cablecar and possibly see Hakone Open Air Museum
and Gotemba Outlet.

Please help in advising best way to cover the above activities via train, bus, etc. efficiently using 2 day pass.

Wondering whether it is worth traveling to Sengokuhara to view 250 images.

As you probably know, the Japan Rail Pass is of no use inside Hakone, but only to get there and back.

Since you want to visit both Odawara and Gotemba, I recommend to use the Tokaido Shinkansen from Tokyo to Odawara, then see Odawara and the sights of Hakone before descending to Gotemba and take JR trains back from Gotemba to Tokyo. Or the other way around.

For transportation inside Hakone, a Hakone Free Pass will probably pay off:
http://www.japan-guide.com/e/e2358_008.html