Changes to my php.ini, httpd.conf, or my.cnf file are not showing up when I restart MAMP PRO.

You must edit the httpd.conf, php.ini and my.cnf files through the Template Editor provided by MAMP PRO. Go to File->Edit Template to edit template files.

If you are making changes to the template file, and they are still not showing up, then check the real files that the template files create.

They are located here

httpd.conf

~/Library/application support/appsolute/MAMP PRO/

php.ini

/Library/application support/appsolute/MAMP PRO/conf

my.cnf

/Applications/MAMP/tmp/mysql