Hi,
You can create a custom field of the table "order" and of the type "text" with the Business edition so that the user can enter a price in the checkout and then, add the line:
$rates[$k]->shipping_price = (float)$order->custom_field_column_name;
(replace custom_field_column_name by the column name of the custom field)
before the line:
if(isset($rate->shipping_params->shipping_per_product) && $rate->shipping_params->shipping_per_product) {
in the file plugins/hikashopshipping/manual/manual.php and the manual shipping methods will all use the price entered in the field by the user.