My site is up and looking pretty and even has some links in it now.
The problem is the links don't work!
I've scoured links.cfg, and the links in that are pointing to the right place.
But on the pages for the categories, the links are coming out like:
<li class="text2"><a href="../../../../links2/cgibin/admin/templates/http://thechaos.net/links/jump.cgi?ID=No">
So I've got something seriously screwed.

Is there somewhere besides links.cfg that could be generating this?

Thanks for all help!
<http://thechaos.net/alert>

The href tag in link.html should be:

Mods:http://wiredon.net/gt/download.shtml
Installations:http://wiredon.net/gt/

Thanks! This put me on the right track.
Since I want the files to link directly to the resource, I used:
<a href="<%URL%> target="_blank">
<%Title%>
</a>