I see...you have a website, or part of the website, in the user's directory. I've never had any experience with that. I suppose symlinks will work. One problem that might happen is if you've configured the server to chroot, although I have no experience with that either...it might still work. The symlinks should persist in a backup.
4) What really is a lib? Closest I can figure is it is like a require or include in Perl. When should something go in /usr/local/lib?
That's close enough an explanation as far as I'm concerned. Libraries are merely code that can be shared by multiple applications, allowing you to make smaller apps and save you from having to rewrite what has already been written. A dynamic library is typically put in one of the "lib" directories because those directories are listed in ld.so.conf. This is the equivalent of how $PATH works for executables. If your libraries are for Perl this probably doesn't apply....I think they should be put in a directory specific to Perl.
5) Where is the best place for log files? They can get excessive in size for persistence.
/var/log, or a subdirectory of /var/log, is the typical place, but I think it depends on what works for you. If you create them in $HOME somewhere, you can add them to .xfiletool.lst to keep them out of your backup.
6) Should Perl scripts to be called from the command line go in /usr/local/sbin?
Probably not. This goes back to the point about sbin being for system admin, not for users.
7) Does a list of auto scanned extensions exist somewhere to see what else is being loaded? It might be handy for Apache2 to auto configure if, say, apache2-docs, Perl, Php, etc... is also being loaded on boot.
/usr/local/tce.installed should show you all the extensions that have been installed. If you check that directory for a specific extension (minus the ".tce"), you can have apache do whatever you need to do if the extension is listed there. The extension install scripts are run after all extensions have loaded, so you won't have to be concerned that the scripts run alphabetically.