Hi Russ,
yes, you have to adapt your coding if upgrading to JCo 3.0.
The JCo API has changed from version 2 to 3.
Please see the JCo 2.x-3.0 Migration Guide for further info.
I suggest that you keep your new Tomcat installation running with the deprecated and unsupported SAP JCo 2.1 until you have finished your JCo migration project.
Please see KBA 1944049 for the download location of the archived JCo 2.1 version.
Best regards,
Stefan