FWIW, there is no train between Takayama and Shirakawa-go, so you have to do the bus for that stretch.
Japan is an expensive country. We just got back from a self-guided trip arranged by Inside Japan. Looking at the ABD itinerary, given all the activities, lodging, and full time guides, I don't think the ABD upcharge is that much more than any other country where you could do it cheaper yourself.
On our trip, we had to navigate trains, buses, subways on our own, forward our own luggage, find our hotels and meeting locations for our guides. It was a lot, but for us part of the adventure. DH and I lived in Japan 30 yrs ago, and DD lived in Korea for 2 years until just recently. For most people, though, it would have been overwhelming.
It looks like a great trip.