It's possible to do a mixture- some tour days, some independent days. That's what I will probably do, although I am waiting to book tour days last minute on days where I'm tired and want to be led around 😁 . And by tours, I mean small local groups or local guides who offer all kinds of experiences.
I feel that a lot of large tours maybe skip from destination to destination too quickly to savour the ridiculous levels of things to do in each area, though. Shorter trips to Fujikawaguchiko from Tokyo seem to be popular, or Hakone. Nikko? Nara from Kyoto? Food tours in Osaka etc. Plus short pre-booked things like tea ceremonies, food tours, classes in making traditional items etc. if you decided against the full tour option. The benefit of a full tour would be that they shepherd you and organise it all, no confusion or being lost, but beware of being rushed or attracting hangers-on who want to walk around with you and be over involved in your holiday just because you're part of the same group (although you might like that potential accompaniment, but it's not for me).
Look on TripAdvisor or Klook to book tours. I've used KKDay app to book the Ghibli park & hotel, otherwise it's nigh on impossible to get tickets abroad. Also, download some translation apps (or Google translate) and Google maps, which will literally show you where to stand on the platform/how full the train is, plus the usual details of what trains to catch, exits to take and so on.
Other helpful solo info is to use luggage forwarding services (takkubin) to avoid taking luggage on public transport. Hotel with 24hr reception, they can book restaurants and help with anything. Staying near the Yamanote line in Tokyo means you'd never be far from a station, following the loop to get around. Look into a JR pass, SUICA card for trains. Carry cash! They use cards much less than some countries. And depending on what time you go, it can be HOT and desperately humid.. Eg right now. Sept is typhoon season. Oct or Nov are good, crisp and sunny.
I've read that hostels can be good for meeting people to go places with, or a night out, but honestly that's my idea of hell 😂 if I was solo, I'd be going full plush hotels/ryokans.
It's possible to look at the itineraries used by travel companies and then tailor it to your own trip (cheaper, more time to savour places). We are doing the usual tourist trail with a few offshoots to other places (the main is Tokyo, Osaka, Kyoto, back to Tokyo) but for a first time, that's more than enough!
Also, Reddit is amazing for reading people's itineraries and trip reports although I've had to step back a bit because its giving me too many ideas and we won't manage to fit them all in..