Many many thanks for such a thorough and informative answers. Some of my dilemmas are now cleared and the trip is slowly shaping.
If my wife agrees, we would try to reach Kanazawa or at least Takamura straight from Nagoya Airport for 2-3 nights in the region. These are anyway connected by bus so we don't need to activate our JR Passes yet.
After that we would hop to Kyoto/Osaka for a night or two.
Than Kyushu for 7 nights with the last night ride to Tokyo. I found on net the following Osaka - Kyushu - Tokyo itinerary:
http://jprail.com/sample-itineraries/kyushu-7-days.html
For our taste the pace is a bit high:
1 day: Osaka - Sasebo, 3 hours sightseeing in Sasebo, Sasebo Nagasaki ss in the late afternoon
2 day: Nagasaka ss, Nagasaka Kumamoto early afternoon, Kumamoto ss
3 day: Kumamoto - Aso - Mt Aso, morning. Aso - Beppu late afternoon. Bepu ss and overnight.
4 day: Beppu - Takachiho morning, Takachiho ss, Takachiho - Miyazaki late afternoon/evening transfer
5 day: Miyazaki - Aoshima transfer, Aoshima ss, transfer to Udo shrine, Miyazaki Kagoshima evening transfer
6 day Kagoshima ss, afternoon transfer to Hakata
7 day Hakata, evening transfer to Okayama to catch Sunrise Sun overnight train to Tokyo
This is CLEARLY too much travel for our taste. 4th and 5th day we believe we should maybe skip, stay a bit longer elsewhere. I also see they are very much south so this is definitely something we don't want to do - spending daytime in travel so much. If we go to Mt Aso that will be pretty enough of nature so we can skip the gorge, also we'd like not to rush so much from Nagasaki or Beppu. Any suggestions for an alternative, slower itenerary? Sasebo - Nagasaki - Kumamoto - Beppo - Hakata (Fukuoka)? Do we miss something important or is there anything spectacular to add along these routes?