Ok, so in short.. any thoughts on how to extract all of these customized core files and put them where they need to be?

While responding. I have downloaded ZenCart to my local machine and have a fresh, running version of it running locally. by doing this I was able to turn on and off the Model Number on Product Listings and hopefully will be able to figure out how to get the functionality from there and place it into my live site.

However, moving forward I want to do this the right way. I want to use this fresh and local copy (and I will even upgrade to 1.50) and want to learn how to add a new theme to it. So aside from Template Monster, could you point me in the direction of where I could get themes to try and install? I just want to learn how the theme / template installation process works so that when Im ready, I will be able to install my own custom theme.

If you're familiar with Wordpress, that process is super easy, you make your theme, drop it in the themes directory and hit "Apply Theme" so I want to learn ZC's version of this.