Hi there!
Your plans already look very good to me! I think that a 7 day JR Pass would be the best option for you, because you can use it to cover all your long distance and pricy travel (with day 4 as starting date). All in all there are only some small things I would change, here they are:
1.) Switch your visit to Harajuku and Nikko around. This way you could use your JR Pass to the max, given that you would start using the JR Pass on day 4. Travel to Nikko can be somewhat expansive when you travel without the JR Pass.
2.) On day 5 when you go to visit Dotonbori, add something else to your plans! Dotonbori is one of the best places to visit in Osaka but it won't keep you busy for a full day. I would add the nearby Shinsaibashi shopping street for sure and if you are interested in electronics/gadgets/anime add a visit to the close by Denden town as well.
3.) The same for day 12, Asakusa is not to be missed but you will have seen everything there after a couple of hours. Why not visit the close by Ueno park, there you can visit Ueno zoo or visit Ginza for some brand shopping.
I hope this helps to improve your itinerary!
-Daniel