You might want to take advantage of the transit without visa facility and have a stopover in Shanghai to be safe. You only need to show immigration your onward ticket print out and they will let you stay for 48 hours.

All China Eastern flights land and depart from the same terminal but you still need to complete the whole re check in process. If you have both sectors ticketed in the same PNR you should be able to hold MU responsible in case you miss your flight as they should have more flights to NRT. However don't count on MU's customer service.