It depends on the region of Japan he was born in. Shinto is highly regional. (even districts have their own gods/ceremonies) It's also not as formalized as Christianity. (It's a Animistic religion with lots of shamanism aspects.)
In general, I've never seen a prayer before bed (except a Christian one). Most of the prayers either involve having a charm or going to a shrine.
You kinda are born Shinto too... Japanese consider if you're born Japanese, then you are Shinto automatically. You cannot convert in... (generally)
In Christianity you constantly have to prove you're a good Christian, but Shinto isn't the same way. You practice it some parts of the year when it's convenient... and the only hardcore people would most likely be priests and their family. (Owners) with the miko and priests as part timers working to sell stuff at the shrine. <-- to explain the difference between systemized and not so systemized.
ETA:
Some resources
Shinto: the Kami Way by Sokyo Ono (Only 11 dollars)
A Year in the life of a Shinto Shrine by John K Nelson (around 15-18 dollars, new)
Both books are helpful. I also read the Nihonshiki online
Shinto Meditations for Revering the Earth<-- Never bought it. There are prayers online, but you really have to pay attention to the region it comes from.
Somewhat The Secret Life of Mariko also goes over basic belief and how religiousness works in Japan. (or the percieved lack of it.)
MC #2 was born in the U.S., but her parents are from Japan.