The issue of detecting malicious code in web pages.

Alright, so this is my problem: for the past couple of months, my host's website (I am hosted on a subdomain) as well as my subdomain has been compromised and injected with malicious, obfuscated javascript that appears to affect *.php and *.htm? files.*

Would there be any <i>safe</i> way to check certain pages (assuming that the attack was automated) for anything that looks out of the ordinary, such as an abnormally long string of hex codes?* I do have a sample saved onto my computer from when I was trying to figure out why my Wordpress installation was going whacko earlier today.