I have been trouble shooting this for a week.

I've been running into problems indexing sites with SPS 2003.

Originally it was a small problem, but in attempting to fix it we've
actually created a bigger problem and now neither my portal_content or
non_portal_content are working. Both indexes have 0 files.
(Previously we have 16,000+ before we began trouble shooting and
messed things up worse.)

The problem appears to be that the index server can't crawl the site
so the index never really starts.

Here is the gatherer log error:
The object was not found. (0x80041201)

I'm running a medium farm with SPS 2003 and WSS 2. The portal is a
SPS portal.

I can create a test portal on this server and indexing works fine!

Now in my trouble shooting with Microsoft Support and looking on the
web a few common resolutions to this have come up.

1. Proxy settings, we don't use a proxy, we never have. I have this
turned off in SPS Central Administration so this isn't the issue.
Also since my test site works, I know this isn't an issue because
proxy settings are for all the SPS portals.

2. Permissions. I've double and triple checked the user is in the
appropriate groups in Sharepoint, on all 3 of my servers. Again since
I'm using the default accounts I setup in SPS Central Administration I
am pretty confident this is not an issue. I know for example that my
test portal on 8080 works fine, and uses the same default crawler account.

3. Alternate Portal Settings. This was at least partially an issue.
And may still be an issue. I originally had two sites on this box.
The ip I'm using now is not the original ip of the machine. It's the
second IP bound to the nic.

4. IIS configuration. I think I've got this working fine because I
have the same configuration for my test site on 8080 as the one on
port 80.

I'm lost here. I spent 2 days on the phone with microsoft support who
were pretty useless.

I'd appreciate any suggestions anyone has to offer. As I mentioned
I've even called Microsoft Support but they don't have very many
people working on SPS 2003. Most of the good guys have been moved to
MOSS 2007 support and unless you're a premier partner you call in and
get newbies that know less about Sharepoint than we do.