Measles and smallpox may have come from China, but recently I learned that the first recorded outbreak of bubonic plague was at Rhapta, Tanzania (modern Zanzibar) in 536 A.D. Therefore the Black Death probably came from the same Equatorial African "hot zone" as AIDS, ebola and the Marburg virus.
Regarding China's prehistory, Chinese tradition asserts that their first fully human king, as opposed to a god or demigod, was Fu Xi, and he came across the mountains from Central Asia and settled at the junction of the Yellow and Wei Rivers in 2852 B.C. If we can trust this date, I don't think we have to do much searching for earlier eras. More likely the missing millennium is a figment of modern imagination, the result of stretching chronologies out to agree with evolutionary thought. Just ask my Freeper friend SunkenCiv; hopefully he will see this thread soon.
A lot was happening at that time.
The Dark Ages: Were They Darker Than We Imagined?
Most of the human affecting diseases will come from Africa, they've had millions of years there to infect humans/primates.