I can add a few impressions on your plans here.
The first thing is not overdo it, especially on your first day. Depending on how much you rest on the flight going over, you might arrive ready to go, or you could arrive an exhausted brain-dead zombie. Not the best for wanting to go around and storm the sights.
For Nikko, I suggest an early morning start, and look into getting the NIkko Pass (or a local bus pass, if you take JR). If you don't mind splurging a bit, get the extra cost of taking the limited express trains to get there faster. It's up to you if you want to get it returning to Tokyo, or just economize and take the slower trains. You can see a number of good places there, but you'd be hard pressed for time to also venture over to Okunikko. It is time consuming and buses are not that frequent. It also has a number of great sights, like Kegon Falls.
https://youtu.be/WWHYZfUr6XkActually, for all your day trips, I suggest you go on a weekday if possible. Some places famous for their autumn leaves can get pretty packed on weekends.
I would also echo what mfedley mentioned about going to Tsumago & Magome as a day trip. I suggest you consider going somewhere else closer by, unless you really have your heart set on going there. It is a huge time commitment round trip, and by the latter part of November the days are already getting pretty short. To add another suggestion for a nice walk, you could try the Akame 48 Falls in Mie. Far more natural beauty than Nakasendo type history though. It's a bit of trouble getting there too, but it doesn't take that long, and in Sakurai, Nara, there are some other lesser known but gorgeous temples to see.
I highly recommend seeing Koyasan if you can. The Koyasan World Heritage Ticket can save you some money and is convenient. But again, save some time and use the limited express version. There is simply no other place in Japan like it. Just don't make the mistake that I did. Like you, I wanted to see Okunoin both during the day and at night. But I found out too late that the temple I was at had an evening curfew (many do), so it completely frustrated my plans. I went in the spring when the days were longer, so you possibly could still do it and get back to your temple (the walk each way can take 30-40 minutes though) with it getting darker earlier, but there is nothing worse than having a ticking clock in the back of your head. So look for a place with
no curfew!
https://youtu.be/uquvCbWANBoTo add a note on endless temples, it is very possible to get "templed out" if you are going around Kyoto. The key of course is to add enough variety in it as well - such as the Toei Eigamura, Iwatayama Monkey Park, Kyoto Station in the evening, the railway museum, some beautiful gardens like Heian Shrine (it's hidden in the back - most never find it), the Shoseien Garden, Murin-an, Jonan Shrine, etc, not to mention the beautiful Imperial Villas (Katsura, Shugakuin, Sento Palace).
There are a number of places in Kyoto famous for the autumn leaves, and you probably know you will be there at the right time (Tofukuji, Yoshiminedera, Rurikoin, to name a few). Most are along the east and west mountainsides. Needless to say, they can get very crowded by people going to see them. There are also a few temples that are only open to the public a few times during the year - one of them being that time, so you may or may not want to take advantage of the opportunity. Plus, some places have special evening hours open to see the autumn leaves as well.
https://goo.gl/knQtMgI would also agree with what was mentioned above that the places trumpeted in all the tourist guidebooks can get swamped with people, and there is no shortage of places that are not as famous but are no less beautiful. But you can still see a lot of the more famous places without most of the crowds if you do things more strategically. Fushimi Inari is open 24/7 and if you go there in the very early morning or evening, you will find few crowds there at all. Same thing for the Sagano Bamboo Grove. And there are some places like Kiyomizudera that open at 6 AM - inconvenient to get up that early of course, but if you are there when others are still asleep, you will find very few people stepping on your toes. Likewise, the Kamo shrines and Honganji temples both open around dawn.
That time of year is the absolute best for the weather - there are far fewer days of rain, and the brain crushing humidity like in the summer is long gone. Nevertheless, you should check the weather forecasts the day before, and as much as possible, keep a flexible itinerary with a back up plan (e.g. museums, aquariums, etc). You will not see it all (nor should you try), but to me, simply getting on a train and going nowhere is a really wasted opportunity. By all means though take some time to just explore the mundane - walk through a supermarket and look at what Japanese people buy and eat - plus the prices they pay. Go to a convenience store and try some of the unique items. Walk through a typical residential neighborhood and see how people live. And skip the bars - just get a can of beer, find a street or park bench, and so some people watching. It can be much more educational than yet another old temple.
BTW - I ran the numbers - and if you do things taking JR as much as possible and your plans the whole way, you would make a 14-day pass pay off very nicely. Not saying that is always the best way to see Japan, as I mentioned above, but if you insist on your plans, the numbers don't lie.
