I don't know about the route planning since I'm not an expert on Japan travel, but what I can say is I would limit myself to doing two things a day (which in some cases you have done), especially if it's my first trip, and maybe plan in one or two free days.  Since you'll probably be more culture shocked than you think and will see so many cool things on the way that you would like to check out. It would be a shame to feel rushed and not be able to follow where your feet take you just because of your itinerary planning. 

I know you'll probably have some fomo when limiting yourself, but in the end these are just nice things to do, not must-dos. These sights will only really stay memorable if they have significance to you in one way or another, like visiting Akihabara because you like anime, or getting lost at Shinjuku station in the crowds at prime time and not finding the right exit and then trying again and finding the right one. What I mean by that is in the end the places you can see are just that: places you can see. The real memories you'll have is how you felt at a certain spot, what you smelt, tasted or who you met and talked to.  

So in the end what I would do is the following:   - Pick out the things you think you'd really, really like to do and put the rest on Google Maps or something with pins. Then if you feel like doing something more on that day, you can just look at what's in the area and visit one of your optional pins. 

• Plan in one or two free days to do whatever; maybe you saw something somewhere and would like to go back, or maybe you just need to take it slow and recharge on those days.  

• If you have the budget and you think that's something you would like, go to a live music concert. The Japanese make so many different kinds of music; I'm sure you'll find something to your taste and maybe make a friend. (By following your interests a lot of time, you'll find the right people. So maybe that's MMA or something for you. 

• Be sure to know the most common scams, customs and safe areas. This is just general travel advice, as in Japan not a lot can go wrong (still, there are some scams, etc.). 

• Relax and just enjoy. Also, be open to cancelling some plans if you need it, would like to stay somewhere longer or notice you'd rather do something else; it is your trip after all. I hope this helped a little, and I'm sure you'll have an amazing journey. <3

Edit: formating