Store form data with file upload in an asset source using Freeform
You could try to use Craft and/or freeform hooks https://solspace.com/craft/freeform/docs/events-and-hooks/#events-freeform-forms and fetch the assets related to the entry during the beforeSaveprocess, add field values of the submission to it and save it again. There are examples how to do this in Crafts documentation 

Or the most flexible (and for me easiest) thing: create a custom controller that extends the freeform controller and add a few lines to attach those information to the asset.