That is a LOT of missing files. I checked my file repository and I only had 277 of the files while i didnt have 671 of them, which is odd to not have that many.
I am wondering if those are old files that where removed by a newer update but wasnt cleared out from the registry.
You can still run all the repairs, just make sure to run them in Windows safe mode and to run all the repairs, do a registry backup first of course.
What problems are you having on the system?
Shane