Ok, so I had been running 5.0.18GA on debian 4 with perl downgraded. I initially went to install and had some perl issues, but after futzing around with Debian, it settled on 5.10 in Lenny and the install went through without any more perl issues.
I then ran into issues of the upgrade not being able to find ldap.bak. The install was resetting it to a 0 byte file. I found a post that said to set the perms to 440 on the file and the upgrade proceeded with only 1 other error: "Upgrading Document templates...failed." I also had some port conflicts but I had Zimbra set up to listen on alternate ports in the old install so I didn't think to much of it.
The upgrade completed and all of the services show started when I do a zmcontrol status. I can't however get either the web based UI or the admin UI to load. The pages just time out. I see port 7071 listening in lsof output but I do not see the https (port 444) listening. When I telnet to the mail port, I get a mail prompt, so I suspect it is accepting and queuing mail.
After looking at the mailbox.log file, I find the following:
"2010-10-26 12:01:55,821 WARN [main]  misc - Could not establish a connection to the database. Retrying in 5 seconds.
com.zimbra.common.service.ServiceException: system failure: getting database connection
I am not even sure where to start troubleshooting database errors.