Ok, so now I’m replying to my own post, but I just wanted to share some information I gathered and maybe ask for some feedback.
For what is worth these are the Japanese Westerns I know about:
Daisogen no wataridori (1960)
East Meets West (1995)
Guitar o motta wataridori (1959)
Koya no toseinin (1968)
Mekishiko mushuku (1962)
Nosappu no jô (1961)
Sandanju no otoko (1961)
Sukiyaki Western Django (2007)
The “wataridori” movies are more like combination of western and yakuza movies, but let’s not be too strict with this, Sukiyaki Western Django was far from traditional western as well. There are more movies in this series, but I don’t know if they contain western elements or not.