1) For some of the DDL changes (changing null to not null for example or
adding an index) in a table forTransactional Replication, I have to first
drop the subscription and publication, make my changes and put publication
and subscription back on. This results in a new scheduled job. How can I
avoid this?

2) There have been times when my replication setup script (generated by SQL
Server) will error out because I haven't run the script to create the jobs
first.

I am doing Bi-Directional replication between a SQL7 and SQL2K box. SQL2K is
publisher/subscriber/distributor. SQL7 is publisher/subscriber. Any help

Adam,
for the replication of DDL, these links should help:
http://www.replicationanswers.com/AddColumn.asp
http://www.replicationanswers.com/AlterSchema2005.asp
I don't have access to SQL Server 7.0 so I'll let someone else answer that
part.
Cheers,
Paul Ibison SQL Server MVP, www.replicationanswers.com
(recommended sql server 2000 replication book:
http://www.nwsu.com/0974973602p.html)