I am documenting our disaster recovery plans and I was wondering if anyone
has any experience with failing over to a log shipping secondary in a
replicated environment.

If I log ship all user databases, and msdb, and distribution to a secondary
server, all to an exact point in time (after disabling all agent jobs), will
replication work on the secondary box? What will break?

I'm thinking that as long as the CNAME is updated so the DNS servers point
to the new box, and the SYSSERVERS table is updated with the new LOCAL server
name, and the account that starts the SQL Server and owns all the replication
jobs is the same domain account, all should be good.

It is too good to be true. Basically what you have to do is enable sync with
backup on your publication database.

Then ship your msdb, distribution, published database to the standby server.
What will happen is your log reader will only read from the log before it
dumps which increases the latency. Now when you failover, you rename the
standby server with the name of the primary and it should pick up where it
left off if you enable the continue on data consistency profile. You may
need to issue sp_repldone incase the log reader is ahead of the distribution
database on the standby. This is somewhat documented in SQL 2000 BOL.

There are more options in SQL 2005. For example with a remote distributor
and if you use the PublisherFailoverPartner.
--
Hilary Cotter
Director of Text Mining and Database Strategy
RelevantNOISE.Com - Dedicated to mining blogs for business intelligence.

This posting is my own and doesn't necessarily represent RelevantNoise's
positions, strategies or opinions.

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The publisher servername is hardcoded into several system replication
tables. You could try renaming the standby server after failover and
renaming the old server, then updating the sysservers table - this should
work.
Cheers,
Paul Ibison SQL Server MVP, www.replicationanswers.com .