Japan the 2nd time around..

Hello! I'm going to Korea for two weeks next summer and decided that since Japan is just a hop, skip, and jump away that I would spend a couple of weeks there as well.
I've been to Japan once before. I was there this past summer and saw Tokyo, Kyoto, Osaka, and Hakone. This time around I'd like to see the places that I wanted to go to but didn't have time to travel to.
This includes: Nikko, Hiroshima, and Nara. In addition to these places, I think I'd like to visit an inaka now that I'm more comfortable and confident in my ability to get around the country. What small town (or simply off the beaten track town) in Japan would you recommend seeing? I think I'd be especially interested in hearing about coastal towns..thanks in advance!

Try Hagi at the south end of Honshu and if you are there in fair weather try travelling the Gono line north of Akita back around to Aomori for an ocean side ride.

Gono line between Goshogawara,Aomori and Noshiro,Akita is really good.
I have found a good webbsite.

http://aomori.photo-web.cc/gonou2/01.html

On my second visit & the only mistake I made was that I should have gome from Tokyo to Nara & then to Hiroshima Instead of the other way round. I found Nara very peaceful and it allowed me time to just be, which would have been even better earlier in the holiday. Other than that I had a fabulous time. I recommend that itinerary. Of course people round here are probably fed up with me going on and on about it :)

If you go to Hiroshima, Miyajima is must.
http://www.miyajima.or.jp/miyakan2/index.html
Tomonoura area in Fukuyama city and Mitarai area in Kure city are worth for day trip from Hiroshima.

Tomonoura in Fukuyama and Mitarai in Kure are the old port towns which are good for day trip from Hiroshima.
http://www.jref.com/practical/tomo_no_ura.shtml
http://www.denken.gr.jp/archives/Hozontiku/mitarai_index.htm...

Asuka is worth to visit from Nara.
You can see a beautiful rural scenery and the old temples in this village.
http://www.asukamura.jp/english/index.html

If it must be a coastal town, try Kanazawa and Otaru in Hokkaido. If you're not that picky, then I would to to Ogimachi or Takayama. The latter would be easier to go to from Tokyo

South of Nara is the Kii Peninsula. You can work down south on the west coast from Wakayama to Shirahama and Kukshimoto, then back up north along the east coast through Katsuura, Shingu, Kumano, Toba, Futami and the famous Ise-shi Shrine before returning to Nara. You can go to the beautiful Nachi Waterfalls from either Katsuura or Shingu. If you're into hiking, you can go for the popular Kumano-kodo pilgrimage route.