Log Included / HDD light constantly on / SLOW Windows 7 Computer

I have a Toshiba Satellite A505-S6989. Specs here: http://www.toshibadirect.com/td/b2c/retail-product.jsp?poid=454117 Its a fairly modern dual core laptop with 4 gigs of ram. I've upgraded the hard drive to a 500 GB Seagate Momentus XT about 2 years ago and upgraded the optical drive to Panasonic UJ240AS blu ray burner. My recent problems happened long after these hard ware upgrades.

I'm running Windows 7 Ultimate 64-bit edition. A few days ago I noticed my computer being brutally slow and the HDD light is constantly on. At that point there were no processes hogging the CPU. I ran an Avast full virus scan both in Windows and at boot. About 10 were found. I originally tried moving to chest but then Avast said there was no room to do this despite having over 100 gb free space. So I deleted all the files and then went back to the chest and deleted the few files that were moved to the chest. A subsequent scan found no new viruses

I ran Malware bytes and it found a few pieces of malware, on the full scan and successfully removed them. A subsequent quick scan found no new malware.

****I've ran SFC /scannow and there are a lot of corrupted files that it was not able to fix despite running it multiple times******

I've ran Seagate Seatools and the hard drive passed without errors.

I've ran Ashampoo registry cleaner and it cleaned about 400 items.

I've ran chkdsk /r /f on all partitions and no errors were found

Attached are logs for OTL by Oldtimer, Security Check, Adwcleaner, Rogue Killer, Malware bytes, TDSAS killer, Hitman Pro, and MG Tools

Some weird behavior I've seen is Carbonite back up says its lost my back up and needs to start from scratch? At one point all my system restore points were erase. Now the new ones do save and don't get erased. There are a bunch of .net 4 windows updates that say they install successfully but then when I check for updates they all come up again as saying they need to be installed.

At this point I think I should just do a repair install as outlined here: http://www.sevenforums.com/tutorials/3413-repair-install.html

If I'm missing anything, going about this wrong, and/or there is an easier or more thorough way to go about restoring my PC to peak performance please let me know. Thanks in advance for everyone's help!

 

Rest of the Logs

Could only post 5 on the first post

 

Thanks for your help. Attached is the JRT.txt log

I'm not sure what those registry entries are. Would it be safe to remove those?

As far as Carbonite I've actually paused the backup to see if that would speed things up and it didn't.

Also, I've noticed i can hear my hard drive clicking. I actually ran the Seatools long test in both dos and windows and it passed both. Currently (prior to running JRT), the hard drive is not making clicking sounds. Seems to be intermittent and Seatools found nothing to fix.

Is it possible that my hard drive is on its way out? If it had problems wouldn't Seatools have found them?

 

Thanks for your help. Attached is the JRT.txt log

I'm not sure what those registry entries are. Would it be safe to remove those?

As far as Carbonite I've actually paused the backup to see if that would speed things up and it didn't.

Also, I've noticed i can hear my hard drive clicking earlier today. I actually ran the Seatools long test in both dos and windows today, and it passed both. Currently, (prior to running JRT) the clicking stopped and the system is way faster.

Could my hard drive be on the way out? Wouldn't Seatools have found bad sectors or seen SMART errors, if this was the case? The clicking seems to be intermittent.