Hi Emma,
Japan is the best place for a honeymoon! (at least if you ask me). With that ind mind, I have made a couple of picks that will give you some a good time together and also don't add too much travel time.
Coming from Tokyo there are a couple of options available.
One would be to visit Hakone, basking in the magnificent view of Fuji, this are is very beautiful and offers much to visit and do. There is nature, temples, onsen and even an amusement park.
Hakone is only a 36min train ride away from Tokyo using the Shinkansen and the JR Pass will cover travel to the area.
After Hakone or straight out of Tokyo, you could visit Takayama. This is a beautiful traditional town, hidden away in the misty Japanese alps. It's a great visit and offers lots in terms of Japanese culture. There are also Onsen close by! Travel to Takayama is very straightforward, first you'll take the Shinkansen to Nagoya, where you transfer to the Wide View Hida Express train. The train ride between Nagoya and Takayama is one of the most scenic in Japan, as the train track follows a river that meanders out of the Japanese alps.
From Takayama it would be easy to return to Nagoya using the Wideview Express.
After Nagoya I would recommend going South west, to Kyoto, Osaka and maybe even further. Kyoto is a must visit, it's the Japanese cultural capital and no visit to Japan is complete without it. Geisha, temples, castle's, tradition, you will find it all. Kyoto is also great for shopping. In addition Kyoto makes for a good base to make day trips from. Osaka, Nara and Kobe are all within an hour of train travel.
Lastly you could visit Hiroshima. The city is nice and Miyajima is one of the most iconic places in Japan.
Hope this helps!
Daniel