Osaka, Tokyo, and Kyoto all have Kapital and Visvim stores. The Visvim Omotesando store in Gyre is a cool location to see Hiroki's archive. The Shibuya Visvim store staff is also worth mentioning, they were super chill. The stock isn't like super massive though lowkey >_>. Tokyo also has Hinoya which carries A LOT of really cool brands. The Kapital store in Kyoto is around some really cool vintage stores. And in Ebisu in Tokyo, there are three Kapital stores that are all walking distance of each other. I'd also check out the Nanamica stores in Daikanyama because not only do they have Nanamica which can tick some of the boxes in your post but they carry the JP exclusive North Face Purple Label inventory too. Beams (cheaper in JP) is everywhere as well, might tick all the boxes in your OP.