If you want to have a time in Kyushu, then I suggest you to time your travel by checking your train and bus schedules. You can do a matrix/tabulation of your travel. On that way, you can plan in advance all your connections and accommodations.
It does not take a whole day to travel on each of your location. You may unload/free up some of days to patch in your Kyushu tour. In the coming weeks, you will see a better picture as you put your schedules, especially when you have early morning or late afternoon schedules.
Check Hyperdia or Jorudan for connections in train travels. Search here in Japan Guide or Google for more information especially for bus travels.
Will you be using JR Pass? 21-day JR Pass I believe will do good in your travel.
When in Tokyo, you may find yourself using IC card (Suica or Pasmo). Take it with you as you can use it on other parts of Japan
http://www.japan-guide.com/e/e2359_003.html. The downside is that the IC card bought in Tokyo can only be refunded in Tokyo only if you opt to.
Tokyo to Nagano to Yudanaka, Yudanaka to Nagano to Matsumoto - I believe you have researched on this already. Nagano to Yudanaka is not part of JR Pass.
Nagano to Matsumoto - an hour away via JR limited express.
Matsumoto to Takayama - Best connection is by bus which is not part of JR Pass. It won't be an easy connection if you travel by train from Matsumoto as you have to travel 1) back to Nagano then shinkansen to Toyama then train [local or Wide View Hida] to Takayama or 2) Shinano to Nagoya then Wide View Hida to Takayama.
I am not even sure about your other itinerary when in Takayama but if you can find time you may visit Inuyama Castle, 2.5 hours away from Takayama. It may not be an easy travel since you have to change train network (JR to Meitetsu). Meitetsu trains are not part of JR Pass.
Takayama to Kanazawa - Best connection is by bus which is not part of JR Pass. On your way from Takayama to Kanazawa thru bus, in between it is Shirakawago so you might detour there. If you insist on train, connect 1) Takayama thru Toyama then shinkansen ride to Kanazawa or 2) Takayama thru Nagoya then Shirarsagi to Kanazawa.
Kanazawa to Kyoto - If you stay near Kanazawa station, you can tour Kyoto after taking the earliest Thunderbird or after 2 schedules as you arrive. Alternatively, you may visit Hikone in between Kanazawa to Kyoto
http://www.japan-guide.com/e/e7003.html.
Kyoto - you may check arukumachi kyoto website on your travel in the city. You may take Otsu/Shiga/Biwako or Northern Kyoto as side trip.
Hiroshima - travel from Kyoto will be ok. Check your schedule if you are planning on going to Miyajima.
Kyushu area - check Japan Guide or similar threads here on what to do there. As already mentioned, you can even fly between Kyushu to Itami
http://www.osaka-airport.co.jp/en/flight/flightschedule/.
Himeji - either take it as a detour before going to Hiroshima or after your arrival in Osaka. Sanyo and Kyushu shinkansens actually stop in Shin-Osaka so you have a better choice there.
Nara - You can even access it when in Osaka. If you plan on visiting Inari to Byodoin to Nara town proper via Kyoto, just travel to Inari or Byodoin from Kyoto and combine it with any other Kyoto itinerary. Better save the Nara town proper when in Osaka.
KIX - Since you still have active JR Pass, you can use it on Haruka express if you connect via Shin-Osaka or Tennoji. However, the fastest in my opinion is the Rap:t by Nankai from Namba or Shin-Imamiya which is invalid in JR Pass (separate ticket).
