I'd like to apply the initialization scripts to the shell which the Perl script is running in.

Note that it's possible to run a perl process from another (non-shell) process without invoking an intermediary shell.

As for setting an environment variable inside a program or script and have that change affect the parent shell, that's a FAQ, both a Unix FAQ and a Perl one (see perlfaq8). See also: export environment variable from a perl program.