Was this the only hard drive? I.e. do you need to re-configure the software for user folders because it was re-installed to default settings?
IIRC NifSkope has a list of folders to look in, set from the Render menu, and it defaults to the Data sub-folders only. I usually add a set of WIP folders for new versions of things I haven't yet copied into the game's folders. If the Meshes and Textures folders you're referring to are outside the Data folder, you'd have to add them again. You probably did it so long ago, you don't remember doing it!
The CS only uses the same folder set as the game, so that one has me confused, although the re-installation could have !@#$'ed something. Do you run more than one version of CS (e.g the old one for lip-sync, and the newer one for everything else?)