I finally managed to apply the custom theme (YES!) thanks to Dede Hamzah's article:
The basic concept is to copy any sass/css/template file that need to be overridden from edx-platform to my theme folder and do my changes as described in above link. One more thing that I did is changing some file names in stanford theme. For example, theme-footer.html and theme-header.html changed to footer.html, header.html respectively so they will override the corresponded files at edx-platform folder (depending on the concept above).
I hope my experience will help someone.