First of all, thank you so much for taking the time to put so many great notes on here! All of this helps me SO MUCH!!!
Tokyo
I really don't have much for Shibuya and Shinjuku so I'll take anything you think we should see. The main thing for Shibuya is the Disney Store. I would like to see Harajuku for Kiddy Land and Meiji Jingu, which is between the two right? For Shinjuku the only thing I have is the Gyoen National Gardens. I know for a fact we will only go to Shinjuku during the day. It just doesn't seem like somewhere we want to be at night. If you have any ideas for either I'll take anything! I mainly put them on here for shopping/sight seeing.
The Disney Store there is really great. You can buy your TDL tickets there IF you don't plan to hop on your first two days. If you want to hop, you need to buy them at your hotel. I agree that Shinjuku is not a particularly interesting place to be at night. Your plan sounds good, especially since you will have time to "get lost" in the gardens & at Meiji Jingu.
Do you think doing the Ghibli Museum, Cafe Hammock, and Odaiba would be a good mix for one day? I think we would want to see Odaiba at night so I thought these three might be good for a one day outing? *On a side note, are there any places we should avoid at night? I read Japan is relatively safe in most places, but it would be good to know if there any we should avoid*
You will be totally safe. Some areas are seedy, but not dangerous, and you won't encounter any of those anywhere you're going. The worst thing that has ever happened to me late at night has been getting hit on by teen boys at the train station & I was alone then, so they wouldn't approach you at all. I have really never felt unsafe. Yes, definitely see Odaiba at night! An idea for you would be to enjoy the Ghibli Museum, stop in at the hammock cafe, check out the new Mori Building Digital Art Museum - which is absolutely not what you think of when you think "museum" (https://borderless.teamlab.art/) & take a ride on Daikanransha (http://www.daikanransha.com/) - there's an English guide in the upper-right corner of the website.
I think we may end up skipping the Skytree. I have to see after editing everything if we would have enough time for it. I'm thinking Shibuya, Shinjuku, Harajuku for one day. Ghibli Museum, Cafe Hammock, and Odaiba for another day. The last day could be the Pokemon Cafe, a baseball game, and any other Tokyo things to see (Edo-Tokyo Museum, Skytree, Senso-Ji Temple). What do you think? Does this seem doable?
Definitely doable. Skytree is highly recommended if you can fit it in but I would prioritize your baseball game & the Pokemon Cafe (because it could end up being a limited-time offering). I would put the Skytree at the top of your "miscellaneous" list.
Do you think Yokohama and Kamakura are possible for one day? They seem kind of far from Tokyo.
It's about 45 mins to Yokohama by train, which isn't too bad. The Cup Noodle museum mentioned earlier is fun, and there's also a ramen museum. Yokohama also has a great Chinatown with lots of delicious food, and some really nice parks. I like Yamashita Park because it's right by the water & you can watch the boats. Kamakura is about 60 mins by train - or, obviously, closer if you're already in Yokohama. I have only been there once, a few years ago - I remember we went hiking, visited temples & did some shopping. It was a great day. The temple I liked best was Hasedera.
Kyoto
I really like Tom Bricker's 2-day itinerary for Kyoto. He has Kinkaju as the first one to visit before it gets too busy. He also has Kiyomizudera as being seen an hour before sunset. I'm not sure if we will be able to time it exactly right, but we are going to stick to his itinerary as much as possible. We are doing mostly touristy things in Tokyo so Kyoto will be more about the nature and temples.
Definitely get to Kinkakuji first, but don't stress about the others. You might like some more & some less. Spend the most time at whichever ones most appeal to you & don't worry about a schedule. You will remember a really great experience more than you will remember checking off a list.
I'm not sure where to fit Wak Japan into. We would only have the two days for Kyoto unless we get rid of Osaka entirely. We may just not get to do it. Dh wants to see Dotonbori so I think we will need to visit Osaka.
Dotonbori is not really that awesome. It's just kind of "what you do" when you visit Osaka. You go to Dotonbori, take the requisite photo with Glico Man, and eat the requisite takoyaki. If you would be in Osaka anyway, it would be a fun thing to do at night. However, I wouldn't go to Osaka just to go to Dotonbori.
It looks like the Gion area is also in Tom's 2-day itinerary so we would be there for sure!
*Another side note, I kind of feel uncomfortable about the whole onsen thing. It looks like something I would love, but I would want to be with Dh if we do it and I just don't know if I could do the whole being naked thing
You shouldn't do it if you're uncomfortable with it! Japanese people think onsen nudity is no big deal because that's their culture, but it's not the culture in the US. Mixed-gender onsen are really hard to find & most couples that want to go in together would do something like book an overnight at a ryokan with a private bath in the room. It's your vacation. Onsen aren't for everyone & you should spend the time doing something you really want to do instead.