In WSO2 API Manager (1.2.0) there are two transports.
1.HttpCore + NIO extensions:Used by api gateway(api).
2.Tomcat servlet transport :used by carbon management console and web apps(store and publishers)
You can change port number of those transports.
According to your requirement,
To change the port of api edit following in API_MANAGER_HOME/repository/conf/axis2/axis2.xml
a)
<transportReceiver name="http" class="org.apache.synapse.transport.nhttp.HttpCoreNIOListener">
<parameter name="port" locked="false">80</parameter>
b)
<transportReceiver name="https" class="org.apache.synapse.transport.nhttp.HttpCoreNIOSSLListener">
<parameter name="port" locked="false">443</parameter>
To change the port of carbon ,store and publisher edit followings in API_MANAGER_HOME/repository/conf/tomcat/catalina-server.xml
a)
<Connector protocol="org.apache.coyote.http11.Http11NioProtocol"
port="8080"
b)
<Connector protocol="org.apache.coyote.http11.Http11NioProtocol"
port="8090"