This is a CSV based on "Japan Government: Gazetteer Japan (2007)".
It contains Place_name, Reading of name (in Hiragana, Roman), Coodinates.
Source data is published at following URL.
http://www.gsi.go.jp/kihonjohochousa/gazetteer.html
Original data may be based on SRS: JGD2000?
They are converted into WGS84, see lat/lon column.
I could not know what is the problem exactory, some points are a little far from proper spot.
Maybe because from my convert, or original accuracy.
At first glance, it probably 1/100,000. Take care.
A. Neither of them. It is published by Japanese Government, based on the resolution of United Nations Conference on the Standardization of Geographical Names, UNCSGN.
A. No need for it.
A. You can do it.
It is recommended that you do acknowledge the source of the Information. A sample attribution statement is "based on '日本国政府(2007): 地名集日本(2007年)/ Japan Government, Gazetteer of Japan (2007)' "