Soft Reject, Need Some Help!!

I have received the following as soft reject points:

  1. Any item in header/footer area that is a function should be moved into
    functions file. Otherwise theme might have issues when users overrides
    with custom templates via child theme.

here is our header code

here is footer code

  1. global variable should be used restrictively and only if theme really must to…( how to do that with SMOF)…any explanation will be helpful