Hard drive issues due to Time Machine backup? Can't source the problem.

Question

Last night my computer began to run extremely slow. All apps simultaneously lagged (spinning wheel of death), but then began working again after about 0.5-1 minute. This whole-system crash repeated about every 10 minutes a total of probably 5-6 times. The last time all apps stopped functioning and (CPU usage of iTunes was 85-95% for some reason (viewed using activity monitor), I am guessing due to its use of multiple hard drives as my music is stored on an external drive) and my computer just shut off after about 3 minutes of completely stalling. Rebooted computer and was left with an EXTREMELY slow system; opening up the quick menu (forgot the name, button on the top row of keyboard) for booting applications took 2-3 minutes. I eventually started disk utility, verified disk. It said I needed to repair disk by restarting my computer while holding down [Command] R message. Made sure i had a backup (at the time of that backup my computer was experiencing the problems above, 11:21pm), so I restarted whilst holding command R. Booted into the OSX utilities, retried the disk repair, received the "Disk Utility cannot repair this drive: back up as many files as you can..." message. Erased/reformatted my internal hard drive, and ran "repair disk" again; disk utility found no problems with the disk. Restored my files to my internal hard drive using OSX utilities (using the full system restore of the 11:21pm backup), and left it running while ran some errands. When I came back to look at my computer, it had attempted startup and crashed with the "kernel error" or whatever where all the text is on the left of the screen. It said something about not being able to find "disk2", which I believe was the disk containing OSX utilities (as veiwed in disk utility while running OSX utilities). Force shutdown, reboot with command R, wiped my internal drive again. Decided to only install a fresh version of OSX in an attempt to scan for viruses (using Sophos Antivirus, running scan as I am typing this), as the slow behavior of my computer had been very strange and began almost instantaneously (seemed like a virus/malware). No threats found so far with Sophos (scanning all my external drives too to source the problem in time machine backups), but I have deduced that there is something wrong with the most current Time machine backup, as it re-established the "problem" (easily fixed once drive is erased using OSX utilities) with my hard drive once I restored it to my internal hard drive. I am wondering (if it is not a virus) if I will need to repeat this whole process with every time machine backup to find where it went wrong, or if i can somehow pinpoint the problem easier. Will all of my Time Machine backups be corrupted now? Why would the Time Machine backup affect the state of the hard drive (does in need to be repaired or not)? Very confused at these random problems. If it is a virus (I will post the results of the Sophos antivirus scan as soon as it is finished), can I remove it from the backup and then restore it with no problems? What do you suggest I do? Will it make a difference to restore the most recent backup (11:21pm) using Migration assistant now that I am running a fresh install of OSX mountain lion? How can I source and eliminate the problem?

Answer 1

Activity Monitor – Monitor Performance Problems  
Performance Guide
Why is my computer slow
Why your Mac runs slower than it should
Slow Mac After Mavericks
Things you can do to resolve slowdowns  see post by Kappy
Try running this program and then copy and paste the output in a reply. The program was created by Etresoft, a frequent contributor.  Please use copy and paste as screen shots can be hard to read.
Etrecheck – System Information