Wow...quite a long post. 
This does sound pretty strange, although it does sound like something is going on with your harddrive. First thing you can do is download a program called HDTune, and run an error scan.
Of course, it couldn't hurt to buy a new harddrive just for safety, they're pretty cheap now... http://www.newegg.com/Product/Produc...SATA%203.0Gb/s
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