Yahoo grabbing old links

I recently re-did my website from scratch. About every day, my logs should that either Yahoo or Inktomisearch is grabbing old urls from my website. This has been going on for about 2 months so far...

I have a custom 404 page. I am wondering if Yahoo is indexing that 404 page as the content of that old link. I just recently set the title to "404 Not Found" ... and I'm hoping Yahoo will get the idea.

And even after months of indexing, the Yahoo cache of my website is still the old one. What gives?

Delete your old files or move them elsewhere to a different directory. The way you described this, the old files you are refering to are still located in the same place they once were and Inktomi is finding them through backlinks from elsewhere.

Well, in both situations, I'm using a master index.php page to manage the links.

Old way:
index.php?top=articles&sub=article_name

New way:
index.php?path=articles&sub=article_name

What I just did a day ago is add a snippet of code to detect "?top=" in the REQUEST_URI, and redirect to my index.php?path=404 page.

You should look into implementing 301 redirects. You can add a rule to your .htaccess file if you are using Apache that can detect if "?top=" occurs in the request URI and redirect to the "?path=" version. This way you will not even need a 404 page and you retain all your link popularity

I guess that is a good idea. One thing I notice, however, is this in my personal logs:

lj1252.inktomisearch.com:66.196.91.32 @ /?top=comical%25E2%258A%2582=noah_ark

I guess that %25E2%... stands for "&sub". Not sure why it has to convert that one part... but yeah, I'll definitely try to look into 302 redirections. Thanks.