Shintoism
Shinto is the most popular and native religion in Japan, that dates back to 500 B.C., and is a polytheistic religion (more than one god). The gods are almost any natural objects ranging from mountains, rivers, water, rocks, trees, to dead notables.

Chief Priest/Kannushi
The chief priest runs the whole shrine and is responsible for all religious observances (religious laws), they are assisted by young female assistants called Miko.

        Shinto Shrines

Shinto Shrines are essentially a place of prayer. You will find all Shinto Shrines with a "torii" at the front there is a photo of one on the right, they are quite iconic, this is said to separate the supernatural world and the real world. The word torii literally translates to "the way of the gods"

The Shrines also have a few other objects on the way into a Shrine such as the Komainu, they are essentially two animals (typically dogs, lions or foxes depending on types of shrines). Komaniu are the protectors of the shrine, they are they are typically located in the inner section of the shrine or even directly inside the shrine 

The "Komainu"

As seen in the picture one of the lions (in this case) has their mouth open and they other closed. The one with it's mouth open is saying the first letter of Japanese あ, and the one with their mouth closed is saying the last letter ん, this is representing alpha and omega, or infinity  
        I gathered much of this information link from here

A "Purification Trough"

There Purificatation Trough is a pool of water that is used to purify yourself by cleaning mouth and hands before entering a shrine hence the name.

   Architecture
The shrines consisted typically of main hall and an offering hall and a stage, sometimes the main hall and offering hall were merged into one

A Main Hall

The Layout of A Typical Shrine

I retrieved some information from here

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A Painting of Nagasaki 

    Differences Between the Two Cultures
From the closed door policy and down to the religion, the culture between the two places were of great amounts.
As said earlier the closed door policy was a big difference, if you are not aware of what closed door policies are it is essentially where nothing comes in (trade, people etc.) and nothing goes out (trade, people etc). This severed both pros and cons for the nation. For starters a pro would be the safety of nothing threatening coming in like disease, threatening animals etc. However this proved that also good things are  not brought in (new weaponry, technology etc). Funnily enough when an English man named William Adams came into the country and brought bits of weaponry and technology, he in a sense revolutionised Japanese warfare.
        The Following is Not to be Taken as Fact
My name is Ryuu 龍 I have escaped from Edo to a dock in Nagasaki, I am about to board the ship.
I have noticed some odd smelling things on this endeavour, from things that people have been eating, like mushy food and watery things, and they're using their hands.                                                                  

A Picture of  Venice in the 1600s

As I got off the boat I noticed the buildings and their odd structure, they have things all over it like rocks shaped in special ways, and the clothing of the people seem to be all types of shapes and sizes, but I do recognise the island like similarities with water surrounding it, however people are using small boats to get around instead of going around the water. It is very odd indeed