You could migrate all the server configuration including the certifcates, they should work just fine. You could check the webMethods_Upgrade_Guide_7_1_1.pdf guide from advantage for more information.
~jk
Also the DOC “webMethods_Upgrade_Guide_7_1_1.pdf” is not clearly meantion about the ports certificates. They have explained about the TN Certificates, Broker Certificates…
Kindly see section Migrate Integration Server 6.1 Data in the webMethods_Upgrade_Guide_7_1_1.pdf. As for the certificates you could use the webMethods certificate toolkit 6.5, or get your private certificate signed by a certificate signing authority.
~jk