If you can't unpack the .rar with the patch files, you can grab an unpacked version from the
Official Site which you just have to download and run.
To find the directories for the files you need to delete, just remember that the .vp subdirectories have the exact same structure as the data folder subdirectories. If you have a file in stu_fs2.vp (voice data) under the personas directory, it'll be in the voice/personas subdirectory in your data folder if it exists and needs to be deleted. Now, going around deleting a that many files to make sure the ones in VPs are used can get tedious though, so if you have the harddisk space and want to get started quickly I'd suggest you to just copy the contents of each VP subdirectory into the appropriate data folder subdirectory, and simply let it overwrite any files with matching names.
Later on you'll want to do it the "right" way (so don't delete the VPs), since having the whole package in the data folder can cause trouble for mods (since they can't override non-VP stuff in the data directory), but by then it'll be much easier since you don't have to look in the VPs all the time, but can rather just delete any large files. Size tells them apart since the files that are there from the HotU installation are simply placeholders with no content, to keep FS2 from complaining when it looks for a voice, animation or other file and finds none.
[Edit] The cinematics are Intro.mve, Colossus.mve, Mono1.mve, Mono2.mve, Mono3.mve, Mono4.mve, Bastion.mve, Endpart1.mve, Endprt2A.mve and Endprt2B.mve.
