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The scan tool would need to be somthing on the order of the the ngs that is Ford specific. This is the tool that the dealers used to use, now they use WDS.
the wds hasn't been used since about 05 the IDS is the latest tool
I just checked a service manual and under the sub-title of GEM Removal, big CAUTION message to upload the GEM module configuration data to a scan tool prior to removal, and then after installing the replacement module, download the data into the replacement module.
That's because a service manual assumes you are using a new GEM with no existing programming in it. So if you don't follow this procedure then the new GEM being blank won't do anything.