I have never tried this. I just know that the PDO supports it:
$dsn = 'mysql:dbname=testdb;host=127.0.0.1;port=3333';
Its actually an additional part of the constructor. If your MySql already knows which port to listen on PDO loads on top of that. I suspect you may not have to add the port as you are not accessing it via a tcp connection but on the local computer. Inside of the my.cnf you set the port for the server. You typically only need the port for remote access.
Have you tried installing it without listing the port?
And something in the back of my brain is yelling to me that there is an advanced database option on the install, but I deal with way too much software to be certain.
Another alternative: is move mssql away from 3306 (if it is using it) and put mysql back there.
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