@top_end_ms - It's really messy to say the least .. even vB's own blog is simply at /blog.php. Some mods that I have are the same way. I hate having random files in my forum root.
I got it working finally. First I copied the client scripts folder into the separate folder I want. Had to copy the /images folder as well (or else no images show up). Then I had to go into the header template and make absolute links for the menu options (or else they came up as domain.com/customfolder/name.php). Still having some issues with the "Search" working on the custom page (keeps going to customfolder/search.php) but other than that, it's as perfect as it will get. Maybe no one will try to search on those pages.

Give it a try!
(Not sure if having two client script folders is going to break anything, security issue, etc? Will find out I guess...)