There are several commands you can run to control the FitNesse wiki, as shown below.  (The values shown between braces are the default values.)

{{{ java -jar fitnesse-standalone.jar [-pdrleoa]
        -p <port number> {80} or {9123 if -c}
        -d <working directory> {.}
        -r <page root directory> {FitNesseRoot}
        -l <log directory> {no logging}
        -e <days> {14} Number of days before page versions expire
        -o omit updates
        -a {user:pwd | user-file-name} enable authentication.
        -i Install only, do not run fitnesse after install. 
        -c <command> Run a Rest Command and then exit.  
            (Return status is the number of test pages that failed as a result of the command.)
        -b <filename> redirect command output.
}}}

You can find more information on the -c options at CommandLineRestCommands.

If you are using SliM, you can also pass in -Dslim.port to hard code the port that the SliM server uses.  This can be used in conjunction with Jenkins Port Allocator Plugin or the reserver-network-port mojo of the Maven build-helper plugin.