My guess is it's an issue with HDD. I've seen similar issues with very old/dying HDDs. For example I have an old knackered laptop that will inexplicably be running at 100% disk or 100% CPU and going really slow.
Run a full CHKDSK on all drives. Also clean up some space on all drives.
Worth checking SATA cables too. Bad SATA cables can cause huge slowdowns (manifests the same way as HDD faults).
In terms of OS I really wouldn't stick with Win7 but if you must, has it been reinstalled since you built the system in 2009?
I wouldn't rule out power either, it might not be total wattage that is the issue more having 6 power connectors loaded.
Finally you might want to consider consolidating HDDs. By which I mean start removing the oldest ones which are presumably pretty small, maybe you've got some under a TB in size still in there?
Run a full CHKDSK on all drives. Also clean up some space on all drives.
Worth checking SATA cables too. Bad SATA cables can cause huge slowdowns (manifests the same way as HDD faults).
In terms of OS I really wouldn't stick with Win7 but if you must, has it been reinstalled since you built the system in 2009?
I wouldn't rule out power either, it might not be total wattage that is the issue more having 6 power connectors loaded.
Finally you might want to consider consolidating HDDs. By which I mean start removing the oldest ones which are presumably pretty small, maybe you've got some under a TB in size still in there?