That is drastic! I did an install just the other day to write a tutorial I have yet to publish and I got nothing like that. I just took the Product Book download and dumped the catalogue section straight into Zen Cart. As it doesn't overwrite any files, the over-ride system isn't really necessary. If you upgraded Zen Cart, none of the product book files would be harmed.

It's getting late, but I'll dig the tutorial out and publish it in the next day or so.