Hi Dean,
Welcome back! I well know the feeling of wishing to go back to Japan and travel!
You'll have many options with a 14 day Japan Rail Pass. You have done all the cities that most visitors will see in their first time. Now it is time to go beyond that! I think there are two broad outlines you could choose from: 1.) Go up north and visit Tohoku and Hokkaido, you can stop at many places like Sendai, Yamagata, Kurosaki, Hakodate, Sapporo and all of Hokkaido. The other option would be to head south and visit Shikoku and Kyushu, here you could visit Takamatsu, Naoshima, Matsuyama, Fukuoka, Nagasaki, Beppu/Yufuin, Kagoshima and more. This route would also travel via Kansai and would allow you to stop at places you could not include before such as Nara.
I think both options are amazing, for now I would recommend reading up on both to see what speaks to you the most, decide and then start filling in the details. You can visit Fuji as a day trip from Tokyo, so that's always on the table.
Let me know if I can help!
Daniel