Flying from San Francisco to Shanghai but 7 hour layover in Kunming (KMG). 3 days then Manila

I'm afraid you are not eligible for 144 hours free visa if you fly USA - Kunming - Shanghai - Manila, because this policy regulates that passengers can only make one stop in China and exit and entry from the same city. But you make two stops: Kunming and Shanghai. If you fly USA - Shanghai - Manila, you qualify for this 144-hour visa free policy.