Transit visa for Indians

We are a group of 15 scientists (all Indians) who are planning to attend a conference in Nagoya (Japan). We are planning to take the China Eastern flight as it is the least expensive among all the options. We shall take the international flight from Kolkata (India) to Kunming. Then we shall take a domestic flight from Kunming to Shanghai (Pudung Airport). Then our next international flight is from Shanghai (Hongqiao airport) to Nagoya (Japan). The return journey will be along the reverse route. All of them will be through China Eastern airlines. There are two places where we are required to go out of the airport in China (1) while going from Shanghai Pudung Airport to Shanghai Hongqiao airport during onward journey (2) In Kunming city because we have 23 hours of transit between two flights during return journey. We are reaching Kunming at 00:55 hrs and our connecting flight is at 23:55 hrs. Do we need a transit entry permit?