Thats kewl then
Glad you've been backing up!
No not really...it'd be messy to do it that way, and I'd have no idea where to start. Plus you wouldn't know which ones, though Windows probably won't boot up without those files.
That means though you have a faulty or scratched Windows disc
You'll have to get a replacement, since the drives obviously having trouble reading it.
By any chance have you got more than 1 cd drive? Try it on the other one if you have, as some drives are more capable of reading scratched discs than others.
If you can't replace the Windows disc, you can get fixers (though only for light scratches, and won't work with deep ones) which puts a gel in the gaps where the scratches are and protects the disc, making it work again.
I hope this helps