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The Jomon are a mongoloid people who made up the population of Japan from 14,000 BC until about 1,000-300BC, when they were replaced by the mongoloid Yayoi people who absorbed them, which is the time when Japanese culture began. Neither of them have anything to do with Europeans.
The skull in the picture does not belong to either the Jomon or the Yayoi, it is an anomaly and may belong to some Ainu.

The Ainu appear to be descendants of Indo-Europeans or Ancient North Eurasians who settled on Sakhalin, the Kuril Islands and Hokkaido, where they were absorbed by the indigenous Yomon population.

The Tocharians were Aryans of probable Yamnaya origin, who spoke an Indo-European language and came to the Tarim Basin from the Afanasievo culture of South Siberia after 3000 BC, and have nothing to do with the much older carriers of the D1a2a haplogroup.

Otherwise Y-DNA by itself doesn't necessarily mean much, there are African black tribes with R1b Y-DNA which means they have an unbroken male line over the centuries to a forefather who was European and nothing more.