I've updated the connector port for Stash via the server.xml file. After starting up Stash, the start-stash.sh script still reports:

Success! You can now use Stash at the following address:

http://localhost:7990/

stop-stash.sh:

Stopped Atlassian Stash at http://localhost:7990/

I'm not sure what else the scripts.cfg file controls, but it would be nice if the server.xml was parsed automatically and all related files updated automatically.