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The only thing that I think you could do would be test it with Scannerz to see if it's got a bad cable or connection in the system. That would show up as long irregularities and maybe an I/O error once in a while. A link to the product is here:

http://scsc-online.com/Scannerz.html

That solution, of course, costs money. Some things you could try for free are to reset the SMC (visit the link before brushing it off):

http://support.apple.com/kb/HT3964

or reset the NVRAM:

http://support.apple.com/kb/HT1379

Another thing to do is make sure that your ssd has garbage collection, etc. enabled. I've heard that the symptoms you're having typical of an SSD that isn't being cleaned up properly. One guy had a video on YouTube showing his system run so slow it was "like I was trying to run off an old CDROM" to paraphrase.

If you try the firmware upgrade make sure you have a backup.

By the way, if you have a backup, is it bootable? If so you might want to try and boot off of it to see if you have the same problems.
 
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