do you have a new perl pet, or just the files you want to subsitute?
making a sfs of the files might complicate things tho... but you could implement a script when you wanted to load the sfs.
schematically, I would
1. run mksquashfs on the new directory
2. locate the resulting sfs to where ever you intend to keep your sfs's
3. write a script that when clicked, would
a. load the sfs, then
b. create the new link /usr/bin/perl that points to the new executable in the sfs.
it would overwrite the existing link, so I would also
4. create another script that would also create a different new link /usr/bin/perl that would point to the target of /usr/bin/perl as it stands now, ie you could restore the original configuration when the sfs is not loaded
just saw your new post,
look at this while I look at that