Fragmentation seems like such a simple problem. Take systems offline and DEFRAGMENT the drive with any one of a number of free tools. In the SQL server world, hopefully you're presizing data/log files, eliminating the need for autogrowth and fragmentation in the first place.
Defraggler or Conrig.exe can both show the fragmentation status of files, without performing the defragementation hence you can see if a drive is fragmented.
You can tell if fragmentation is affecting your disk throughput by monitoring the following counters -
LogicalDisk\Split IO/sec or PhysicalDisk\Split IO/sec
Technet : Examining and Tuning Disk Performance