@Caleb323 - I don’t think you can remove any fields from the XML file created in ERP that Manifest use.
Did you ask ship support for help? Dave and Phil should be able to help further troubleshoot via a webex. I am a bit confused as to why you want to remove the To Company name. what if you had to ship to another company ship to location? I think it would be a bad idea to try to remove it.