The sad thing is I left the rail passes behind. Terribly upset. Consolation is I can get a refund. But would have like to have the passes instead.
Now we have to plan and cost every trip.
For example, Train from Narita to Tokyo. 900 yen. Narita to Funabashi 520 yen on the Keisei line then switch to JR rail. The Funabashi to Tokyo was a 380 yen trip.
The confusion for us was Keiseinarita was the same as Narita station. Sort of. Just that the line was run by the Keisei company. Same for Keiseifunabashi and Funabashi station. The 5 minute walk in the Hyperdia website advice was simply crossing over from one platform to another but exiting and entering another gate. So in that sense it was a different station. But Keisei line simply refers to their stops as "Narita" and "Funabashi", without the "Keisei" prefix. But for preciseness, Hyperdia makes that distinction. Once you understand that, it is less confusing.
Later we took the train to Haneda Airport. For once Hyperdia failed us, it was unable to recognize the other stations and only had directions from Tokyo station, to Hamamatsucho (150 yen) to change to the Rapid Monorail to Haneda (450 yen).
From Haneda we flew to Memanbetsu Airport but was worried about how to get to our hotel in Abashiri. There was a bus, but the schedule was subject to change. Fortunately, the hotel was near the Abashiri Station and the bus was quite regular. The bus took us and only collected fare at the end of the Journey. The bus had a bilingual announcement system that announced the stops as they came up. When the system announced our stop, we just made some worried noises and the driver asked us something in Japanese and we answered in the affirmative and he dropped us off at the right stop, and pointed the station out to us.
No worries about change. The driver was able to make change with the machine on board.