toonetcreation about modification you've done, will be lost on next template upgrage?
You can isolate the settings and customizations by making use of local folder as defined here and have the specific JS file which has been edited be copied to local folder path which will enable the same to avoid from being overridden
when the page is loaded, the header background is dark instead of being transparent = not ok, when scroll down, the header background is transparent with opacity = ok perrfect
Kindly check now. You will see the similar styling of affix menu for other pages as seen for homepage now
Ensure to clear your browser cache if changes dont reflect.