well, what you do, is install Windows, put it in Audit mode, update, install, all that. for finishing touches on the after-install, you'll need some startup scripts to do the rest. or thats how i do it. i lost my sysprepped Windows install, so it depends, you just need to do some testing, for it to actually work.
the preinstalled apps after sysprepping, still work, but if they write in HKEY_CURRENT_USER, youll need to find a way to copy those registry entries over to the new user profile after installation