http://technet.microsoft.com/en-us/library/cc966539.aspx

http://searchsqlserver.techtarget.com/tip/15-SQL-Server-replication-tips-in-15-minutes

http://www.sql-server-performance.com/2005/replication-tuning/

Master DB rebuild and change check list

1. backup login script http://support.microsoft.com/kb/918992
2. backup linked server script
3. Detach databases.
4. Master rebuild whatever option
   • create another instance and attach : make sure same file location of system DBs, msdb, master, tempdb(you can fix it later).
   • single mode rebuild : http://blogs.msdn.com/b/psssql/archive/2008/08/29/how-to-rebuild-system-databases-in-sql-server-2008.aspx
5. When you rebuild or attach master DB, you should know about sa password from original instance.
6. SQL service pack update if different version.
7. Attach databases
   • If you move master database from other service, you should drop unnecessary databases.
8. run #1 login script only for necessary account(s).
9. change sa password if you want
10. change master key with force option

    https://simonsql.com/2012/02/23/an-error-occurred-during-decryption/

    ALTER SERVICE MASTER KEY FORCE REGENERATE

11. change server name
    http://msdn.microsoft.com/en-us/library/ms143799.aspx

    use master
    declare @srvname varchar(255), @new_srvname varchar(255)
    set @srvname = @@servername
    set @new_srvname = 'new hostname'    --your computer hostname
    exec sp_dropserver @srvname
    exec sp_addserver @new_srvname, local
    go
    

12. change server option if you want to change : sp_configure
    • min max memory
    • ad hoc query
    • e.t.c.

I guess, you had a problem on Master database.
After changed you got linked server error like this.

“An error occurred during decryption.”

The reason why login mapping password can decrypt due to master key changed.
So, you need to generate again master key with force option.

http://support.microsoft.com/kb/914261

ALTER SERVICE MASTER KEY FORCE REGENERATE