Windows Update will not install

Hi expert, recently I have restored the computer to the factory setting (windows 7 64 bits) since the virus destroyed my registry and I couldn't install the MSE. It seems everything is OK now.
But I have over 114 Windows updated files which cannot be installed. I tried updating the driver software from the device manager and trouble shoot  following the Microsoft Fix link. Then I manually updated these files. It first installed service pack 1 and it  seemed working, but it took forever to update one file. Then finally it finished and  restarted the windows. But it took forever to shut down. Then I turned off the power. After I turned it on again, the system showed Windows 7 Service Pack 1: Failure Configuring Service Pack, reverting changes error and it went on and on without stop on the screen and never ended. I waited for a long time and finally the windows restarted  and it showed it had 114 files to be updated and it looked like they were updating. But when the updates was finished, I turned on the machine, the 114 files were still there, not a single file was installed.
Before Windows 7, when I format my drives, I only insert the bootable disk to the CD drive and then everything will be installed from CD when the machine is turned on. But when I insert the CD into the CD drive and turn on the windows 7 this time, the CD will not boot at all. Does it mean windows 7 does not need to use the bootable disk? We just restore to the factory setting instead. Do I have to format the c dive first and then restore to the factory setting? Please advise! Thank you!

>Windows Cleanup seems to have done the trick, though before trying it I actually managed to install LR 2.0 beta with no problems. Anyway, since it's a windows system, anything can happen -- and frequently does!
But that is what happens; you may get an error trying to install one particular application while all others work perfectly well. The cleanup utility fixes the problems for that particular application and saves you doing registry edits etc.
>I have install issue saying I dont have the right Window Installer error when I install 1.4.1 update too.
If you do not have the "right Window Installer" you may need to download the latest version from Microsoft. You can find the revision of your current windows installer by looking of properties of Msiexec located in c:\windows\system32. My version is 3.1.4000.1823.
This is the link to the download:
http://www.microsoft.com/downloads/details.aspx?FamilyID=889482FC-5F56-4A38-B838-DE776FD41 38C&displaylang=en
Also, make sure that your Windows is up-to-date.

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