Not sure yet about the I/O's. I may use mini extensions like you say or might just make new openings with a dremel. I can make rubber plugs for the old holes out of Sugru if i want to block them or make up something with my MakerBot Replicator when it arrives next month.
As for the models, you can get them online and just import them into whatever 3D app you use. But it's important to get the specs for the Game Boy and change the dimensions of the model to match as none of the models I found were correct and I didn't have time to create one from scratch. If the dimensions aren't correct then its pointless to do any work in any 3D app.
I used Google Sketchup Pro for the animation I made but am using a more professional application for the real modelling.
Just a note to mention I'll be tracking my progress in the mod and repair section of Retrovia if anyone wants to keep an eye on it or contribute any thoughts on anything.