Well after restarting my computer again it worked perfectly. Your best bet is probably to just keep trying.
I am trying to update my iPhone to iOS 5 but after it backs up my phone it say error (-5000) and says if I continue I will lose everything on my phone. Anyone know why it does this?
Temporarily disable your antivirus software. I had the same issue trying to install iOS 5 until I read some other posts. It worked for me, and I use Microsoft Security Essentials on Windows 7. I tried installing iOS 5 three times and got the error (-5000), then disabled Microsoft Security Essentials realtime protection, then it upgraded to iOS 5 just fine. Be sure to re-enable realtime protection after your iPhone/iPod/iPad update.