For security reason,  for read only fields, only the values configured in default value or populated using Forms calculation or lookup rule will be submitted. So value populate using custom JavaScript won't be submitted.

You can have either keep the fields as read only and change from JavaScript calculation to Forms out-of-box Calculation or you can uncheck the "read-only" option from the field settings but use JavaScript to set it read-only as following:

$('.readonly input').attr("readonly","true");