I concur with Robbie. Though would classify the mentioned as large production makers, yet did have their special handcrafted models.

For specials or exclusive handmade makers, could go further back to the mid or late 1960's. One example would be Kageyama. He likened the fine Italian frames and eventually honed in on their racier geometry.

Getting back to quality production bikes from Japan, I think the main thing first noticed was a better finished product. The lugs less sloppy, nice uniform paint. And for components -no issue as Suntour was on top.