The second bus was also 3-seater, almost all the same except there were no hoods and the motif is Mocha and brown instead of dark pink and gray. No toilet but you don't need one coz it stops at service stations twice. We arrived Shinjuku at around half past six in the morning.
It cost 9,300yen from Sannnomiya to Shinjuku coz they charge extra 2500 yen during peak season.
From Shinjuku back to Sannnomiya, I decided to take the cheaper bus which was only 7,300 yen (also plus 2,500 yen) but I REGRET. There was not enough leg space and the baggage space was too small for my regular sized backpack. I can't put it in the baggage compartment coz my macbook was in it. At 4:00 a.m. despite the human heat, it got cold inside. The insulation was not enough to keep us warm when the outside temperature dropped below zero. There was a toilet but there's no way that you can go without disturbing others. So if you're not on a tight budget, I suggest you pay extra 2,000 yen.
From Shinjuku there's a bus to Kofu City, Yamanashi Prefecture. My Singaporean friend insisted that I visit him there and that he'll pay for my fair. All the buses were already fully booked, so I took the JR express train. The regular fair was 2,060 yen plus 1;300 for the express ticket, non-reserved.
On my way back, I took the bus. It takes 1 hour and 40 minutes by train and 2 hours by bus for only 2,000 yen (3,000 yen for round trip). There were not many passengers, only 1/4 was occupied. I slept the whole 2 hour trip.
My friend's girlfriend drove us to Kawaguchi town where we could have a good view of Mt. Fuji. The Houtou noodles, pride of Kofu City was delicious and warmed us up.