Since my last build much as changed for my project. I started by creating a function that would count files and record them along with directories and build a small Wix script based on them. I tried to create a dynamic script that would package an extension and add it to an existing script. Unfortunately I learned that its almost impossible to combine two Wix scripts so I was somewhat at a dead-end. That is until I realized that I could use my new function on the Firefox directory as a whole. I tried it and with some bug fixing (by some I mean hours) I was able to re-invent my project but far more powerful.
Now all you need to do is point the program at your Firefox install directory and it makes an .msi file based on your Firefox. This means that all you have to do is install extensions,configurations or add-ons and as long as they are in your Firefox directory my program will package them all together and create an .msi file.
1) Firefox must be installed
2) Wix must be installed
Note that this build has been tested but its also likely that there are still tons of bugs. For my 1.0 build I will have these sorted out.