FYI, I had the same problem.
Except I was unable to find the IndexAgentPerfCounters files on the source Media of MsExchange 2013 With SP1. I founded on MsExchange 2013 without SP1.
after, When I tried to Run : New-PerfCounters -DefinitionFileName "E:\Program Files\Microsoft\Exchange Server\V15\Setup\Perf\IndexAgentPerfCounters.xml", the New-PerfCounters was giving me :
-----
New-PerfCounters : The term 'New-PerfCounters' is not recognized as the name of a cmdlet, function, script file, or
operable program. Check the spelling of the name, or if a path was included, verify that the path is correct and try
again.
At line:1 char:1
+ New-PerfCounters -DefinitionFileName "E:\Program Files\Microsoft\Exchange Server ...
+ ~~~~~~~~~~~~~~~~
+ CategoryInfo : ObjectNotFound: (New-PerfCounters:String) [], CommandNotFoundException
+ FullyQualifiedErrorId : CommandNotFoundException
-----
I solved this by running
Add-PSSnapin Microsoft.Exchange.Management.PowerShell.Setup
after I was able to run :
New-PerfCounters -DefinitionFileName "E:\Program Files\Microsoft\Exchange Server\V15\Setup\Perf\IndexAgentPerfCounters.xml"