I was able to get it to pop up briefly in the correct spot by changing.
$( "body.woocommerce-checkout .ywgc_enter_code" ).insertAfter( ".woocommerce-form-coupon" )
to
$( "body.woocommerce-checkout .ywgc_enter_code" ).insertAfter( ".coupon-form" )
However, it disappears quickly once the form is fully loaded! The field that pops up is only about 25% width as well.