Using the night trains with a JR Pass is always a bit tricky and cannot be relied on when making your plans as you are unable to place your reservation for the train before you get to Japan. It's hard to give any specific guidance on making reservations on the sleepers other than "leave yourself as much time as possible" as you were planning.
If you are set on using a sleeper, how about moving the Hokkaido trip to the very end of your journey after your travel to Hakone and Yokohama. This way you'll have a breather around Tokyo before embarking on a trip north, and will give yourself maximum amount of time to reserve a place.
Both Hamanasu and Akebono night trains have free accommodation for JR Pass holders. In terms of the quality of the free accommodation they are much the same (extremely minimal - carpeted area + sheet/pillow. The Hamanasu slightly edges it here I think as it has heated carpeting), but the Akebono is a longer (and more balanced) overnight trip. Personally, I think I'd go for the Hayabusa to Shin-Aomori and Hamanasu to Sapporo option. I also think there is more chance of reserving this train.
If you are planning on going to Hakone for 1 day only you may be better off just purchasing individual tickets from Odawara as needed. For example, Odawara to Sounzan is just over ¥1000 each way. This is in contrast to the 2 day Hakone Free Pass at ¥3900. Bear in mind that you'll still have to pay for Hakone Ropeway (¥1330 round trip from Sounzan to Togendai) and also for the Hakone sight seeing cruise as needed, but tickets could work out as a slightly cheaper, (but less flexible) option.
Hope this helps!
