Joel, thanks for the good news. Did you get an idea from your friend what the root of the problem finally was?
Here's a concise run-down of my experiences with some of my WordPress 3.0 installations (not WordPress-mu) under C-panel in case it might be of use to anyone.
Backups, of course
I disabled my plugins
I deleted any leftover junk in wp-content/upgrade
I ran automatic update to WordPress 3.0. (may take several minutes)
Sometimes it would hang and then give the "Briefly unavailable"
I would remove the .maintenance file from the website's
I would do the upgrade manually.
I would run http://mysite.com/wp-admin
If it worked, great. If not, I'd try to see if I failed
to follow the instructions somehow and correct.
Most of the time, it finished with success.
After the core upgrade, there may be plugins or themes to update.
Again, I delete any leftover junk in wp-content/upgrade, and for me,
the core upgrade has always left behind some stuff there.
About 25% of the time, I found my automatic theme updates worked.
The rest of the time, I found they failed, so I would delete and
Upon doing any automatic update, I found a failure of any kind could
leave behind a .maintenance file which i would remove,
and then sometimes I would just do a shift-refresh to redo the
update or try to bring up the desired page again without losing
the data along the way.
Once the plugins and themes are updated, I would attempt to
turn the plugins back on.
I would also clear the cache for DB Cache, Super Cache, or on my
VPS without C-panel, I would clear the W3 Cache and turn it back on.
I would then go to phpmyadmin and optimize any tables with overhead
and analyze all the tables again.
I might then go back and pre-populate the caches and log out just to see if everything runs fast and looks good.
Does this sound like a healthy and effective approach?