The first question that I have in mind before continuing this post is:
Q: Is it possible to have multiple instances for the same SharePoint farm?
A: Yes it is possible, we can have more than one SQL instance where we can store the content databases.
If you want to transfer a SharePoint content database from one instance to another you can use the following procedure:
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Before starting implementing performance counters, be sure you are not using one of the following options:
– /3GB switch – is not supported http://support.microsoft.com/kb/933560
Reducing the size of the kernel mode memory buffers when in /3GB mode causes unacceptable
performance in Windows SharePoint Services file-transfer operations.
– Web gardens – http://support.microsoft.com/kb/822171/ IIS 6.0 Session State May Be Lost If You Use Web Gardens with ASP Applications
– Priority Boost on SQL server – http://support.microsoft.com/kb/319942 How to determine proper SQL Server configuration settings
By default, the priority boost setting is 0, which causes SQL Server to run at a normal priority whether you run SQL Server on a uniprocessor computer or on a symmetric multiprocessor (SMP) computer. If you set priority boost to 1, the SQL Server process runs at a high priority
Once you have removed all those options you can start implementing performance counters and start analyzing them.