Look for your errors in %windir%\Logs\CBS\CBS.log. It is more verbose and can help you find something that doesn't show up in the System Update Readiness Tools log.
I can't really blame Microsoft on this one. From my experience it is third party tools, software, or drivers themselves that are deleting the critical files that the service pack install is looking for.
Well I put back every missing Ati driver file, double checked file permissions, got a clean bill of health from update readiness tool, uninstalled my antivirus, renamed distribution folder, ran sfc /scannow, removed firewalls, used msconfig to uncheck 3rd party services and startup apps, ran a virus scan, installed other prerequisite patches, studied the cbs log and still nothing. SP1 can go to hell. I dont care anymore. This Service pack is total bs!