I found the solution to my own problem. openpyxl is a library contained in a .egg file. py2app and py2exe don't play nicely with .egg files. Once I unzipped the .egg file and placed it in my project everything worked nicely. Also my setup.py file didn't need to be nearly as complicated, below is the setup.py that works. Also, I stopped building it in alias mode and it worked just fine.
"""
Script for building the example.
Usage:
python setup.py py2app
"""
from setuptools import setup
setup(
app=['notebook_tracker.pyw'],
setup_requires=["py2app"],
)