There may be instances when you would like to modify the default ports used by commerce toolkit or commerce server, here is a short blog on how this can be achieved, I prefer option 1 which requires simple edit of configuration file, in an environment with webservers you will have to generate and propogate the plugin file from app server to webservers.
Make changes by directly editing the configuration file which stores information about ports
Change the value of port to a desired value, save the file and restart server
<specialEndpoints xmi:id="NamedEndPoint_1183121908101" endPointName="WC_adminhost_secure">
<endPoint xmi:id="EndPoint_1183121908101" host="*" port="9043"/>
<specialEndpoints xmi:id="NamedEndPoint_1183121908102" endPointName="WC_defaulthost_secure">
<endPoint xmi:id="EndPoint_1183121908102" host="*" port="443"/>
Make changes from WAS admin console as shown in screenshots below, save your changes and restart test server.