Messing around with the Winsxs folder isn't to be recommended in general - the drivers
folder is a bit different, as it does have backups.
I would **never** delete stuff - renaming it is acceptable and easy to do from RE, since it seems basically to ignore permissions (you can easily replace/delete/rename files owned by TrustedInstaller at least, without having to mess with permissions)
All updates will make significant changes to the COMPONENTS registry hive - it may be worth copying that to a working machine and loading it to examine the changes there using something like RegScanner (NirSoft) which can search by modification date.
You could then compare the file structure found with what's supposed to be present according to the hive.
(Arduous work but I suppose it could be semi-automated?)
</thinking - it hurts too much <g/>