I firstly want to point out that other log frameworks can be used with no problems, but you will not have the ability to configure logging for your application through the console if you use your own handlers/appenders.

1.  Where does the log4j jar file go?

If you want to use your own configuration file you need to package log4j in WEB-INF/lib in your WAR file.

2.  Where does the log4j properties file go?

Same place you would normally put it for a log4j. In a WAR IIRC it should be in WEB-INF/classes.

3.  Do yo have to modify the server startup file(standalone.xml)?

You don't need to modify standalone.xml at all. You will need to include a jboss-deployment-structure.xml with your deployment though. You can get more information on that here https://docs.jboss.org/author/display/AS71/Class+Loading+in+AS7#ClassLoadinginAS7-JBossDeploymentStructureFile

Your jboss-deployment-structure.xml would look something like the following.

<jboss-deployment-structure>
    <deployment>
    <!-- Exclusions allow you to prevent the server from automatically adding some dependencies -->
        <exclusions>
            <module name="org.apache.log4j" />
        </exclusions>
    </dependencies>
</jboss-deployment-structure>