What time of year?

Where are you flying into/out of? The most efficient way would have you arriving at one of the major international airports and departing from another to avoid backtracking. The classic is in through NRT or HND and out through KIX or vice versa, but others will work.

You seem to have locations scattered throughout the country. By design?

Are you sure you want to stay in ryokans for the bulk of the trip? In my mind, they are wonderful for a night or two but for a honeymoon trip, I'd definitely schedule more nights in decent hotels - with beds and en-suite baths.

For that long and that wide afield, I'd think the 14-day or even 21-day Japan Rail Pass would be a must. Trains are ubiquitous throughout Japan, from little one car rattletraps to the famous shinkansen bullet train. For a trip like this, you will undoubtedly be using all types.

Since you want to "immerse" in the culture, you should probably trim your list and plan on several days at the major stops. For my first visit years ago, I spent over a week in Kyoto and could have used more time. My second trip, I did the same in Tokyo. Rented a small place with cooking facilities, found the nearest grocery and moved in, mostly riding subways or buses and walking the areas that interested me. Since then, I've pretty much covered the country but don't tend to stay in one spot so long anymore. You may not want to go that far but you will probably need several days each for Tokyo and Kyoto, a day for Nara, 2 or 3 days each days for Nagasaki and Hiroshima and Miyajima. The list goes on.

For such a trip, I'd recommend getting a tape or book course and learning a few words and phrases of Japanese. You probably won't use it much in the big cities but it would be handy in smaller towns. I'd also get a good guide book with map and plan your route to most efficiently connect the points you want to see. From your list, which includes some unusual choices, I'd guess you already have something like that. I've never heard of some of your list but I see that you haven't included some of my favorite areas like Matsue, Kanazawa, Takayama, all of Shikoku Island, Fukuoka, Kummamoto, etc. I used to recommend Himeji and Matsushima but the first is under reconstruction and the second was devastated in the tsunami <sigh.>

For rail routes and costs, try www.hyperdia.com .

There are some very well-traveled folks here. I'm sure you'll get some good suggestions.