Thank you all for the replies, and apologies for my tardy response. An excess of work resulted in not being able to think about the fun things!

Pureboy - Thanks for the suggestions, taken the point of only changing hotels once between Kyoto and Kobe, I think we'll base in Kyoto and Osaka and day trip from there. We may head further south, and skip Shikoku Island. Next step is pick up a guide book and properly map this out.

Freccia - Budgeting around £500 for Noribetsu for the two nights, and we'd both appreciate a ryokan style room, with good dining, and a good Onsen. This is looking ideal, http://www.kashoutei-hanaya.co.jp/en/cuisine-en/. Food wise, we love everything. Tend to have a preference for street food, and usually we go for more casual options over Michelin stars. Eaten in starred restaurants through the USA, Europe, and Asia, I'd take a quality Turkish doner or Pho most evenings. Looks like Akita might be a nice break in the journey from Hakodate, but might require skipping Sendai. Any opinions on this?

beep88 - Thanks for the extra spots, will check them out when the guide book arrives.

The other half is a real art buff, so the Art Site should score some well needed brownie point.

Thank you all again for all your help!