See my limited inline response...
1 - I get a synchronization exception  error (event ID 202) every 30
seconds. No idea why and I can't even find anything that could lead
me further in my research, much less a solution. Any ideas anyone?
[Reply] No idea, sorry.

2 - I was working on alternate authentication using CAC (Smart card)
It wasn't working properly so I decided to unextend the site and
start from scratch. I checked off all the boxes which come up to
delete the IIS website as well as the content DBs and I also went and
removed SharePoint from the website (Application management - Remove
sharepoint from website - chose the application and selected the
proper one from the dropdown). I recreated in IIS alone, instead of
letting MOSS do it, set up CAC authentication and when it worked I
went to extend to it again. When I selected the new site MOSS told
me that it was already in use by MOSS... I've looked everywhere and
cant find a reference in any of the options so I am stumped. Can
anyone help?
[Reply] Not sure why it wasn't removed, but I'd guess that you still have
a reference in one of the tables in the config database. Start by
looking at the sites table, then the VirtualServers table (in v3 it is
probably called the WebApplitions table. Be sure to backup the database
before you delete the offending record. This is a test/dev environment,
right?

1 - Still no idea so if anyone runs across a solution or at least a
clue please let us know and I will do the same.

2 - No reference in db, anywhere, but I resolved the problem on a
fluke and I'll share in case anyone runs across this issue
themselves. Turns out that it wasn't registering a duplicate on the
site, it was the port number that it was registering as already being
in the DB. I have one IP and multiple applications that I bound to
that IP on port 443 and using host headers. This was done using
cscript and the adsutil. On a whim I entered a different port number
when I was trying to extend the site again and it worked. To make
sure that it was this I recreated the scenario and sure enough it
failed until I changed the port number. FYI - if you use cscript and
the adsutil MOSS will NOT change your port number in IIS if you use
another one in the application configuration, although it says it
is. My 3 methods of authentication are working properly (AD, CAC
(smartcard) and Forms) so now its on to troubleshooting why my LDAP
authentication using ADAM isnt working. I may come back on that one
too but I want to TS a little more myself first. I've only put in 2
1/2 days on that one so far :-/

This is an "almost" live 60GB portal instance... We were
depreciating this portal so I moved it to its own front end, gave it
its own set of DBs on the back end and did an in place upgrade. Now
I am attempting to configure the alternate authentications as well as
TS problems  we may have with our other portals later on when we do
the real rollover. As long as I have access to the data we're good
to go. Nothing new going in and I have multiple backups I can
restore from if everything goes south. My other 5 portals are safe
and sound in a stable, high availablity, SPS 2003 solution...

Makes sense that a duplicate port number would return the same error as
a duplicate host header. Just harder to find. Glad that you were able to
find it.