I have decided to make a separate topic from my main question asked in http://www.bleepingcomputer.com/forums/t/541509/hdd-problems/ because no one in the thread suggested for me to do a repair installation. This thread is primarily concerned with some concerns I have regarding a repair install and is separate from my "main" thread.
My sfc /scannow scan in the elevated command prompt never makes it past 71% verification stage, so I though that a more thorough repair of system files was in order. I followed the instructions provided here: http://www.sevenforums.com/tutorials/3413-repair-install.html but was concerned when they said to "extract the Windows 7 SP1 ISO file to a folder on a partition or HDD other than the current Windows 7 partition". Does this mean I cannot run it from the C:/ drive?
I hastily extracted the repair install into a USB. It went fine until the first restart, where it tried to boot up from the USB. I fixed this by changing to boot order to boot from the hard drives first. However the system setup was unable to access the files, presumably because the USB driver was not running. It this a reasonable cause, or am I just making newbish guesses? I don't have a CD large enough to burn the Media Refresh to.
I strongly appreciate all the help I got from my first thread and hope that I haven't broken the "don't ask the same question twice" rule. I am posting this question separately because it is mostly a different issue.