I managed to solve the issue with the file upload edit. Not sure if this is the best way.

This post helped with the idea: https://our.umbraco.com/forum/umbraco-forms/93241-umbraco-forms-custom-upload-field-store-string-value-of-file

        string fieldFolder = field.Id.ToString();
        string newFolder = DateTime.Now.ToUniversalTime().ToString("ddMMyyyyhhmmss");
        string dir = "/media/forms/" + fieldFolder + "/" + newFolder + "/";

        IList<HttpPostedFileBase> files = context.Request.Files.GetMultiple(field.Id.ToString());

        var existingFile = context.Request.Form[field.Id.ToString() + "_file"];

        foreach (HttpPostedFileBase file in files)
        {
            if (file.FileName != "")
            {
                // Create directory
                if (!Directory.Exists(HttpContext.Current.Server.MapPath(dir)))
                {
                    Directory.CreateDirectory(HttpContext.Current.Server.MapPath(dir));
                }
                // Save the file
                file.SaveAs(HttpContext.Current.Server.MapPath(dir + SafeURL(file.FileName)));

                // Add string to the form       
                myValue.Add(dir + SafeURL(file.FileName));

                //force close the file to avoid error in accessing the file
                file.InputStream.Close();
                file.InputStream.Dispose();
                GC.Collect();


                // Remove any old file
                if (existingFile != null)
                { 
                    string oldDir = existingFile.Substring(0, existingFile.LastIndexOf("/"));
                    // Remove old directory
                    if (Directory.Exists(HttpContext.Current.Server.MapPath(oldDir)))
                    {
                        try
                        {
                            Directory.Delete(HttpContext.Current.Server.MapPath(oldDir), true);
                        }
                        catch
                        {

                        }
                    }
                }
            }
        }
        // If nothing has been added but a previous value exists  add to the list
        if (myValue.Count() == 0 && existingFile != null)
        {
            myValue.Add(existingFile);
        }

        return myValue;