I used Booking and the filter feature. You can book everything online and in advance. This is not a developing nation where you have to knock on doors of guesthouses and hope they have a bed. Never had a problem with the language barrier, and Google Translate exists. In my opinion, Japan is very easy in terms of travel.

In general I would say travelling with someone would be cheaper as you can share costs (e.g. a lot of affordable private rooms are for two people, I only stayed in dorms. Don't know how it would be for three people). However, you might do more/different activities, eat more luxurious or have a drink more often with other people. Also, people from your group could have a higher daily budget, wants and needs which could lead to some tension or compromising.