Late to this game, but just in case you're still waiting on your dev...

Magento has an automated add-on system called Magento Connect, and you can access it from your admin (unless the original installer disabled it on your account). You can just use that to install Yoast's plugin. Check out http://www.magentocommerce.com/magento-connect/canonical-url-for-magento.html

Aside from that, if you are using something after 1.4, you should have canonical built into your store (it's in the config section).

If you're not using something after 1.4, consider upgrading. It's not painless, but anything prior to 1.4.1 is pretty rough to use. I'm not surprised you've got bugs and general sadness.