Hi there!
I think you'll find the travel you have listed for the 2nd and 8th pretty hard going (or even impossible). How about considering doing one of your list rather than rushing around all of them?
Aside from that, it looks like an interesting trip!
If you keep your current plans I recommend activating the JR Pass on the 30th. Bear in mind that Tokyo station exchange office opens at 7:30am, so you'll need to adjust your plans to compensate for this I think. you can use it on the express train for Niseko, however be aware that if you activate on the 30th, the last date of use for a 7 day pass will be the 5th of Jan. As you intend to travel long distance on the 6th-8th, I recommend the following options:
- Rather than get a flight from Hakodate to Sapporo, get a flight from Haneda to Sapporo. This price will probably be the same. Then aim to start a 7 day JR Pass form the 2nd to the 8th. This will cover all your long distance travel as you travel down the country and back up to Tokyo/Haneda
- Purchase a 14 day pass. Although you won't be in Japan for 14 days, it will be more economical to purchase a 14 day pass than to pay for the JR ticket cost for the travel you detail from the 6th to 9th.
I hope this helps you make a great plan!