Hey there, hope this help ( just came back from Hokkaido self drive)
1. for your D1 which route you plan to use? If same as mine, you will be reaching Asahikawa first, so you will need to drive to Furanu/Biei and back to your hotel (1 hour+ one way) Or the other route, you will be driving a lot more hours. How about staying in Furanu instead? Suggest you stay at least 2 night in Furano (if you are into Flowers, melons, lavender, country side and mountain)
2. Noboribetsu and Lake Toya are nothing special, worth a detour but not a full day, you may visit them while on your way to Hakodate.
3. Spend at least 2 nights at Hakodate, you won't regret it.
4. Skip Niseko
5 Day trip to Otaru but no need overnight. Stay at Sapporo instead. Sapporo to Otaru is just around 45 minutes. Spend 2 nights in Sapporo

6 Every souvenir, chocolate, or Hokkaido limited stuff are available at the Airport at around the same price. So, don't worry if you forgot to buy anything.

Staying overnight in Lake Toya to see the fireworks display. Noboribetsu will stop by for day trip. Considering to stay 2 nights in Hakodate now