Ian Kerkemeyer

While I wasn't able to download my custom field values, I was able to add and update them with a file upload in my sandbox environment. I don't have the file ready for production just yet but I will do the update once it's completed. I went to Admin Center-->People-->Import organizations-->Had "Update existing organizations" checked. My file included the organization name and the three custom fields. One was a drop-down field and the other two were text fields. 

The only caveat was the organization name had to be exactly as it is in Zendesk otherwise a new organization was created.