If you use a dynDNS service you don't need the PHP script changing the address of links on the whole site, just update your IP address each time it changes. The problem I see, with a WiFi shield you're usually behind a router which does NAT for the whole local network. So you cannot use the IP the Arduino got for the dynDNS update. Usually this is done by the router anyway, your router doesn't?
Show us the code you're currently using and describe what exactly happens when you run it as well as what you expect it to do.
The last part of your post sound to me like you're trying to access a web page but forget to set the "Host:" header line.