How many deadlocks am i really getting? system health or deadlocks/sec?
From a reliability standpoint of deadlocks per second the perfmon counter will be more accurate.  The system_health monitor is based on ring buffers which can overflow over time or miss events if there is enough activity within a brief period in order to facilitate reliability.  There is a file that backs this which you can look at which will give you more history but if you are experiencing as many deadlocks as you are indicating there is a distinct possibility that you may not have full history within these.  This would explain your discrepancy between the two measurements, you aren't doing anything wrong from what I can see.

The files will be located in your SQL Server install directory under %Program Files%\Microsoft SQL Server\MSSQL11.[Instance Name\MSSQLSERVER]\MSSQL\Log\system_health_*.xel.