I had Windows Vista 32 bit until the other day something went wrong. I kept getting (Not Responding) problems. Sometimes it would just be for a minute, sometimes I would be able to move the mouse but not click anything, others the mouse simply wouldn't respond. I ran chkdsk and that seemingly reset Windows settings. Same problems though. Another chkdsk and I couldn't get to the desktop due to a missing file.

So I bought Windows 7 since the computer didn't come with a Windows Vista disc. Installed it and got an error, \Windows\system32\winload.exe is missing or corrupt. I managed to run chkdsk. After that it installed and got to the desk top. HOWEVER, I'm still getting the (Not Responding) problems so everything runs super slow. Seems like it does it if I'm doing multiple things. Also, when I reboot it attempts to do a chkdsk that I can't skip until it's down to 1. I'm afraid it's going to delete files that don't need deleted. 
 
Someone recommended I do a completely clean install since I had some old files under a backup folder. I did that and I'm still getting (Not Responding) all the time. It will freeze and no matter what I click nothing will happen.... until suddenly it will do everything at once. 
 
I tried installing updates but I got  "Failure configuring Windows Updates." 
 
Help?

Unfortunately, I have no advice for you since I'm a Windows XP using dinosaur, but I eagerly await all the "lol use mac" posts to follow.

I think I formatted. It deleted everything off of it. I went by this,
  http://pcsupport.about.com/od/operatingsystems/ss/windows-7-clean-install-part-1.htm
 And yes, it is a legit version.

Stuff missing/corrupt in the system32 folder should have been fixed by a clean install of windows 7. 
The whole slow down thing might be a result of low RAM, or you may have a virus - failure to configure windows updates indicates that RAM is not the real issue. 
 
Which leaves a virus as a real possibility, but from my knowledge, a complete wipe of your hard drives should fix that. I suspect that the clean install of windows 7 may not be as clean as you think.

If you know you did a clean install, it's a hardware error.
 
If you've got a Dell PC, you can boot into the diagnostic mode and do all sorts of tests 
Get and run Memtest
Get and run One of these, depening on harddrive brand
Do a stress test
Look at the logs in windows (Right click my computer -> Manage -> Event viewer) - it's unlikely you'll find anything there, but...
If all else fails, bring your computer to someone who can help you.

it might be your hardrive that has gone haywire. Could you test it?

I've run the memory test several times and it didn't come up with anything.
 
Under Event Viewer I've got a Kernel-Power error under critical. 2 of those. Under errors there is WindowsUpdate, SideBySide and Eventlog.