The biggest problem with renaming your modules is, of course, the many references made to your module throughout your code. It's usually a fairly morbid experience to grep through thousands of lines of code and make sure all names are correctly changed. Global search and replace makes this easier, but the problem can be pre-empted in initial development.

my $pkg = "My::Package" ;
eval "use $pkg ;"

#you can also reference the package base class from a var
my $obj = $pkg->new ;
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Now you can easily change the package names just by changing the definition of $pkg.

I hope that helps.