- Scripts and styles should not be hardcoded anywhere in your theme or added any other way but with wp_enqueue_* hook and to be added from the functions file. This includes custom JS/CSS.
Example(s) from your code and there are more:
header.php - http://envato.d.pr/1fEQx/4d9dOIgS
It’s funny because when I start making this blog WordPress was in version 4.4.2 and this function exist from 4.5.
But what should I do ? how send to JS variable from header ?