The latest version of Tor browser bundle will use random ports when connected. Just look at the message log to see what port the socks listener is on and use that number in Bitcoin settings.

If you need to remain anonymous that your even using Bitcoin I guess you have no choice but to download the whole blockchain through Tor. Otherwise you could download the whole chain normally then connect to Tor and then send your payments you want to send through Tor.

But as mentioned it's the addresses and how they are associated outside the network that is usually where the anonymity is lost.