If you are currently using setuptools in the setup.py for your project, and making use of python setup.py bdist_wheel as the method to generate the .whl file, add the following line to the MANIFEST.in file which is already present at the root of your project.
recursive-include myproject *
Naturally, replace myproject for the actual top level directory that will include the target .pl scripts (or any other file).
As a demo, if your setup.py is written approximately like so:
from setuptools import setup
from setuptools import find_packages
setup(
    name='myproject',
    version='0.0.0',
    description='demo package',
    long_description=open('README.md').read(),
    classifiers=[
        'Programming Language :: Python',
    ],
    packages=find_packages(),
    include_package_data=True,
    zip_safe=False,
)
Running python setup.py bdist_wheel will show output that looks like:
...
adding 'myproject/__init__.py'
adding 'myproject/config.py'
adding 'myproject/logging.ini'
adding 'myproject/myperlscript.pl'
adding 'myproject/scripta.py'
adding 'myproject/utils.py'
adding 'myproject/version.py'
adding 'test/__init__.py'
...
The files are packaged inside the .whl:
$ unzip -t dist/myproject-0.0.0-py3-none-any.whl 
Archive:  dist/myproject-0.0.0-py3-none-any.whl
    testing: myproject/__init__.py    OK
    testing: myproject/config.py      OK
    testing: myproject/logging.ini    OK
    testing: myproject/myperlscript.pl   OK
...
Installing the resulting .whl file in a new environment:
$ pip install -U myproject-0.0.0-py3-none-any.whl 
Processing myproject-0.0.0-py3-none-any.whl
Installing collected packages: myproject
Successfully installed myproject-0.0.0
$ ls env/lib/python3.6/site-packages/myproject/
config.py    logging.ini      __pycache__  utils.py
__init__.py  myperlscript.pl  scripta.py   version.py
Also note that if the MANIFEST.in method is unwanted, include package_data={'': ['*']}, argument for the setup call should also make it work with the recent versions of setuptools.
Further addendum: The setuptools package actually has a MANIFEST.in that include this particular syntax, though restricted to specific filename extensions for the files they want to include.  This is clearly a supported option despite some guides/documentation that might suggest otherwise.  In fact, this is a feature provided by the core distutils module that is shipped with Python by default.  Related questions: