Internet Explorer on Win 7 won't open after malware removed

Hi Experts,
Have a Windows 7 PC.
Tried to remove some annoying pop ups, and other with Malwarebytes.
It found several instances of malware but didn't remove the popups.
Ran Hitman Pro which has helped in the past when this happens.
Now IE won't open.
It opens in Safe Mode
Ran SFC/SCANNOW
Tried to open without third party extensions.
Just get a spinning comet for a second then nothing.

The main icon for IE in the Start Menu was changed to shortcut to a different page.  I copied the iexplore.exe to the start menu.

Hitman found 2 proxy servers.  

Wajam was one of the programs that was removed.
all of the instances in the history of both scans reveal PUP in the description.
PUP.Optional.BrowseSafe.A
PUP.Optional.SearchProtect.A

Thanks in advance for your assistance.
LVL 3
sgt_bestAsked:
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TropicalBoundCommented:
Open Control Panel / Internet Options
Click the Advanced tab
Click the 'Reset' button
Click 'Delete personal settings'
Click the 'Reset' button
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sgt_bestAuthor Commented:
Same result.  Attached are the malware logs of what was removed.
I could open the browser before the scans.
HitmanPro-20140903-1341.log
protection-log-2014-09-04.xml
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JohnBusiness Consultant (Owner)Commented:
If the IE Reset fails to work, try:

1. System File Checker:  Open cmd.exe with Run as Administrator and run SFC /SCANNOW. Allow to complete, run a second time and restart the computer. Test IE.

2. Run a Windows 7 Repair Install:  You need the Windows 7 DVD to do this. Here is a Seven Forums Tutorial to assist with the repair.

http://www.sevenforums.com/tutorials/3413-repair-install.html
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sgt_bestAuthor Commented:
John Hurst, Since I just ran SFC/SCANNOW once and restarted do I need to run it two more times?
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JohnBusiness Consultant (Owner)Commented:
SFC does not always correct all errors. That is why I suggest running it twice.

You ran it once and restarted. Does IE work now?  If yes, no need to run SFC again. If no, try it again but it IE still does not open then you need to try a Repair Install.

One other thing to try:  Create a new, test Windows User Account (Profile). Log in as the new account. Does IE work in a new account?  You could have a damaged windows user profile.
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sgt_bestAuthor Commented:
Ran it twice with nothing found each time. Reboot no joy.
Attempting the repair install.
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JohnBusiness Consultant (Owner)Commented:
Also try the new user profile as profile are very easily damaged.
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sgt_bestAuthor Commented:
New user has the same issue.  ie won't open.
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TropicalBoundCommented:
From the Run menu, try:

iexplore.exe -extoff

This will start IE with no add-ons.  If it does open, there is an add-on problem.
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JohnBusiness Consultant (Owner)Commented:
Let us know about IE in safe mode, but not likely based on what you have said. It is entirely common for a virus repair to damage a machine beyond repair.

So probably your best solution here is to back up and reinstall Windows.
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TropicalBoundCommented:
Another possibility would be to navigate to Programs and Features, view installed updates, and uninstall the Internet Explorer update.  Reboot, then have Windows Update reinstall IE.
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sgt_bestAuthor Commented:
PC was a Sony Vaio and the "Vaio Care" stuff comes up with the disk differently than the link in the solution however I was able to navigate to a repair install.
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JohnBusiness Consultant (Owner)Commented:
@sgt_best  - Thank you and I was happy to help.
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