More information on PanAm's first trans-Pacific flight
There are many sources of information about these flights that you can find by doing an Internet search. For example, I just used "panam clipper flight sfo to mnl".  

The following links should get you started:

In addition to some aircraft information, this link has a schedule image about halfway down the page:
https://www.pacificaviationmuseum.org/pearl-harbor-blog/pan-ams-pacific-clippers/

This link has more Manila-specific info, with a video. 
http://www.lougopal.com/manila/?p=1463

The following link, in the paragraph "Building Bases Across the Pacific" will answer your last question regarding MDY/AWK:
http://www.clipperflyingboats.com/transpacific-airline-service