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Sorry about that, I got a little confused with BuildMaster's configuration... there is no appSettings.config file for ProGet :-/
ProGet's website port is determined by arguments passed to the service. If you stop the ProGet service, run ProGet.Service.exe as administrator, and choose Uninstall, the service will be uninstalled. You can run it again and choose "Install" to add it back, then it will ask for the URL to reserve, and you can enter something like http://*:1000/ to reserve all hostnames on port 1000.
Make sure to choose an identity that has access to the SQL Server database. If you chose Network Service as the account to use when you first installed, just leave that as the default option for the user account when prompted.
If the service takes a while to start up (i.e. longer than 5 seconds), it probably means the user account assigned to run the service does not have access to the DB (it could take a minute or more to time out). Just reinstall the service in the same manner to host with a different user.