A foreign is Looking to fly from Tokyo to Beijing then on to Kuala Lumpur with a about a 60 hour layover in Beijing. China Eastern routes the flight from Tokyo through Shanghai. Am I still OK for the 72 hour VISA free transit in Beijing or does Shanghai become the city I arrived into China from?

1. You will have to go through customs in Shanghai.
2. When you arrive at Beijing, the fly has been changed to Domestic route.
3. According to the 72hr TWOV rules, it would not be ok in Beijing, because for the Beijing customs, it is not the international inbound. At the same time, it also not be ok in Shanghai, because it is not the international outbound.
4. conclusion: you should fly to Beijing directly from outside of China and go out of China directly.

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