In the meantime I'm using Applescripts to do the same thing and invoking the unix shell from the AppleScripts to do things that are clumsy in AS.
Note, with regard to the recursive copy module, I have modified it to use MacOSX copy to insure that the meta data AND the files are copied. The recursive copy module only copies the file info.
Try going in and manually deleting the files in the old tree. Then rerun the install. Perl might still be seeing the old version.
5.6 and 5.8 are not binary compatible, so you're likely to run into this with other modules as well. You'll have to manually delete those modules to install the new ones successfully.