If you want to visit all three parts of the shrine, you would normally get off the bus at the lower shrine, visit that, hike 2 km to the middle shrine, visit that, hike 2 km to the entrance to the upper shrine, and then walk 2 km on the path that leads to the upper shrine and visit that. Then, to get back you need to retrace your route 2 km from the upper shrine to the bus stop at the shrine entrance area and get on the bus for Nagano. The bus only runs about once per hour, so make sure you have a bus schedule and donft miss the bus you want. It will likely be on time.
Note that I have gotten the 2-kilometer measures from Japan Guidefs description of Togakushi. These estimates seem about right to me. There are also some other hiking trails, including one that goes to Kagamiike (Mirror Lake). I have gone there twice and had marvelous galettes at the cafe therec
How much time you want to spend at the individual shrine complexes is up to you, but they are not like temples where you go inside and potentially spend time admiring Buddhist treasures or attending a ceremony or something. They are basically structures out in the woods, with places to offer devotions or pray (you can learn the customary way to do this at a shinto shrine if you want, but it wonft take a big bite out of your schedulec). So the bulk of the time will be spent on the hiking/walking trails. These are beautiful, and the reason I go to Togakushi in the first place. In season, there are lovely wildflowers in places, and I always spend a fair amount of time admiring them along with the trees and other aspects of nature there.
I guess for starters you could think about out how long it would take you to walk the minimum four 2-km segments (lower to middle, middle to upper entrance, upper entrance to shrine, and then back to the upper entrance bus stop. This is assuming that 2 km is an accurate measure of the trail lengths (again, this seems about right to me) and that you wonft get lost anywhere like I once did (but I didnft have a map with me).
To do all of this, obviously you want to get as early a start as possible, and you probably donft want to spend too much time at the lower shrine (or you could skip it and get off the bus at the middle shrine), and you will need to pace yourself while walking to make sure you finish the whole course in time and donft miss whatever bus you want to take to get back to Nagano.
If you donft want to do this much walking, you can take the bus from the lower shrine to the middle shrine and/or the middle shrine to the entrance of the upper shrine. Again, timing is of the essence; if you miss a bus you have a long wait for the next one.
Obviously, if you really want to do this excursion, especially as a day trip from Tokyo, you are going to want to prepare in advance, download maps and an up-to-date bus schedule, and pick a day with decent weather. You will spend essentially the whole day walking, and while the trails are not particularly strenuous, you need to prepare to be outside all day (in a glorious environment but one with only bare minimal support for tourists).
It is of course possible to skip one or more of the three shrines. On one of my trips there I just went to the upper shrine, visited that and then hiked to Kagamiike and had a delicious galette :) and then walked back to the upper shrine bus stop (getting slightly but not hopelessly lost) and then went back to Nagano. This was enough for me, but if youfre coming all the way from Tokyo to see Togakushi you might want to visit at least the middle and upper shrines.
In short, I would prepare extensively, get a very early start and allow all day (you do NOT want to be finishing up after dark, and you do NOT want to miss any buses). Togakushi from Nagano is a fairly easy day trip with some room for errors. From Tokyo, not so much.
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