Thanks for the feedback. I have written an application to parse an Excel spreadsheet containing the data about all of the pins (including subsections for labeling). The software generated all of the correct terminals and both copper layers, but I couldn't figure out how to get my XML output to work with Fritzing. I was trying to "hand make" an .fzp file. I realized that I'd have to have something to start with and then open it up and replace the < connectors> element to get everything correct.
The first release that I did was all manually adding the connections (and data) to Fritzing using the part editor (ugh). Now, with my application, it's easy to change the part connections. I just have to make sure that all of part layers have the same connector/terminal numbers for the pins.