Note: I feel obligated to state that, at this point, your best deal is likely to just get a JR Pass. Your Tokyo to Kyoto journey will cost 18,000 yen, while your Osaka to Hiroshima journey will cost you another 10,000. If you also need to return from Hiroshima to Tokyo, you should seriously consider getting a JR Pass. If you have a JR Pass, then there's no need to worry about anything below.
You can do Tokyo to Kyoto via Nagano and Kanazawa easily. Here is the route you want:
Tо̄kyо̄ --- via Shinkansen --- Nagano --- via Shinkansen --- Kanazawa --- via Hokuriku Main Line, Kosei Line & Tо̄kaidо̄ Main Line --- Kyо̄to
If you can read Japanese, use a ticket vending machine and buy a base fare ticket. It will let you choose the route you want. Then, buy all the required limited express tickets as you go; I usually do it right before I take the train. The limited express train that runs between Kanazawa and Kyо̄to is the Limited Express Thunderbird (特急サンダーバード).
If you cannot read Japanese, your best bet is to show this to the person at a ticket vending window:
東京 --- 北陸新幹線 --- 長野 --- 北陸新幹線 --- 金沢 --- 北陸本線・湖西線・東海道本線（特急サンダーバード）--- 京都
Your base fare ticket should have something like this printed:
経由: 新幹線・長野・新幹線・金沢・北陸・湖西・東海道
Note that you don't actually need to list all your stopover points. As your ticket is for a very long trip, stopovers are simply allowed, unless you disembark within Tokyo or Kyoto. However, stopovers will invalidate your limited express ticket if you have one.
Your second itinerary will work out, but very tightly. Osaka to Hiroshima is 337.8 km, and by JR rules your base fare ticket will be valid for exactly 3 days.
