Companies for Self-Guided Tours in Japan

Are you using the Fodor and Frommer guides for Japan, or Lonely Planet or Rough Guide? They will have info such as this.

What help, specifically, are you looking for in "arranging a self-guided tour"?

I don't mean to be snide. It is quite easy to arrange your own personal, self-guided tour from your laptop in the US. Hotels can be booked, train routes researched, tickets bought in advance (although not necessary for most journeys and most times of year), flights obtained. If you have specific concerns, I suspect there are several here who can assist with resources for researching or booking various aspects of your travel.

For starters, have you taken a look at these websites? Good info from general to more detailed. The above recommended travel guides are good also. Even if you eventually use a paid traveler planner, you will want to have some idea of what is available and what you, personally, might want to include in a trip.
https://www.japan-guide.com
https://www.japan.travel/en/us/

As a starter, you might take a look at this description of the "Golden Route" which is often the start for first time travelers. It hits what many consider highlights and a traveler can easily branch off this to other locations. (I don't think the included detailed itinerary is particularly good for Tokyo or Hakone, but once major destinations have been determined, deciding on sites at each location that of special interest becomes much easier.)
https://www.japan.travel/en/in/itineraries/golden-route/

Thanks, ORDTraveler and Phred.

I know that I can make all my travel arrangements on my own, and by using the websites you mentioned and a Moon guidebook, I already have a general idea of the region and places I would like to visit. in Japan.

In considering the use of a tour company, I was looking for someone who can offer a pre-arranged itinerary that is practically workable (i.e., not overly ambitious or logistically challenging) , with pre-arranged Japanese accommodations and travel arrangements chosen by someone who knows much more about Japan than I do--and a "one-stop shopping" aspect to it. Call me lazy, but this has some appeal and value to me, as I bring no particular local knowledge to the Japan trip planning process even though I have the ability to book all of these arrangements on my own. I'm not sure that in doing my own research about accommodations in, say, six different cities and the transport between them I can come up with a better trip than a company might offer (putting aside the time I would have to spend doing the research and making all separate bookings).

The company "Japan Experience" is one that--judging from its website--seemed to offer what I was looking for, and I was wondering if anyone has any experience with it, good or bad, or with other companies offering similar services. Thanks!

I get it! I understand time pressure.

Here is a fairly recent discussion that might be of interest to you.
https://community.ricksteves.com/travel-forum/trip-reports/has-anyone-travelled-to-japan-with-samurai-tours-recently

Thank you! There are so many (interesting) posts on this forum that it can be difficult to find the most relevant ones.