Peter, I had my Illustrator Artboard set on Pixels as the unit of measurement. That was causing it to export the SVG incorrectly. I've since changed all of my source files to Inches and re-exported them. I put them in Fritzing (after some resizing of the schematic - it was HUGE). The PCB is still off, I wouldn't trust it.
Also, I figured out how to get my custom application to generate all of the pin < connectors> XML for the .fzp for me (including connecting to the terminals), so I feel a lot better about making changes now.
Honestly, I made this part so I could show the breadboard connections on blog entries and articles on the Mojo. I thought it would be inconsiderate not to at least provide a schematic. However, getting the PCB board correct may be above my level at the moment. It's just two 50 pin headers and one 10 pin header, but the arrangement has to be perfect to line up and I don't even know how I set the drill hole size in the first place. 
I've updated the GitHub and added an issue to fix the PCB.
Thanks for your help, it's a big challenge and having someone to assist along the way has been marvelous.
I'm probably going to have to start from scratch on the Schematic to get the spacing correct. It's a little better now, but the pins are still off. I've written scripts in Illustrator which help with pin numbering, so it's just a matter of getting the spacing correct to match the connector0terminal, connector1terminal, etc.