Don't forget the view that northeast Asians (Ainu) mixed with South East Asians (Malayo-Polynesian speaking peoples) to form the Jomon People. The Jomon People then inhabited the Japanese archipelago until the great migrations of southern Chinese and Koreans mixed the melting pot a bit more to form the Yayoi People.

I've recommended it before and I will recommend it again: J. Edward Kidder, Jr.'s "Himiko and Japan's Elusive Chiefdom of Yamatai" provides a *fantastic* view of Jomon, Yayoi, and Kofun period Japan.