I have completed the first working build of my project. It is the Firefox Packaging Tool. To properly use please read the following...
1) You must have the Wix tools installed for this to work (this build only)
2) Options such as changing the homepage and adding extensions DO NOT work yet. (next build)
3) The tool assumes FireFox is installed in the default directory (only this build) and that you are running a Windows OS
Install the software using the installer. When the program loads simply click the "Create .Msi" button and let the software do its thing.
I've also made a list of the files added to my new Wix build.