Buddhism*: 63%
Catholicism: 30%
Shintoism: 7%
*A combination of various sects, including Shintō-Buddhist sects.
Strictly speaking, Shintoism is generally not considered a distinct religious category in Japan itself, since Japanese Buddhism is generally considered to incorporate most of the practices of Japanese folk religion (aka, Shinto). The concept of a distinct Shinto religion really emerged during Imperial Japan, when the government went to great pains to try to "split" it from Buddhism and describe it as a civic ethos (and Western scholars described it as a religion).
The question of whether Shinto is even a religion is controversial in Japan itself and there's a pretty tortured case law about this. Japan has separation of church and state, but a lot of Shinto festivals are government-subsidized under the rationale that they're "local traditions". One of the constitutional revision goals of Prime Minister Abe Shinzo is in fact to classify Shinto as essentially not a religion (at which point the government would fund most of the Shinto shrines in the nation). I don't think either side of this divide would actually classify Shinto as a distinct religion. Abe and friends say it's not a religion (but rather traditional cultural practices), and his opponents more or less classify these practices as just part of Japanese Buddhism.
- Japan will have the same proportion as the OTL percentage of Christians in South Korea at around ~30% Catholic in the present day, mostly concentrated in Kyushu, Chugoku, Tohoku and Hokkaido.
Also yeah, I think Christianity would at most peak at 25-30% of Japan, because that's where it's at in South Korea, and even that basically took a very unusual turn of events to make happen. However, in the vast majority of scenarios where Sengoku-era Catholicism survives in Japan, I actually don't think it hits anywhere close to 30% (my guess is 10-15%, much like pre-Communist Vietnam). The difference between Korea/Vietnam is that in Korea, Christianity was very much strongly associated with national liberation, while that doesn't quite work with Japan and Catholicism from Portugal/Spain. I think it will always have that sense of being somewhat foreign.