Laying out one PCB, sending it out to a fab, stuffing it with components, and having the whole thing actually work when you’re done is a solved problem. Doing the same thing and having it plug in to another PCB… well, that’s a bit harder. Forget about building a PCB and having it fit inside an enclosure the first time.
The usual solution to this problem is printing the board to be fabbed on a piece of paper, take some calipers, and measure very, very carefully. Extra points for sticking a few components you’re worried about to the paper before lining the mechanical prototype up to the existing board. [N8VI] over at the i3 Detroit hackerspace had a better idea – print the whole thing out on a 3D printer.
[N8VI] is working on a software defined radio cape for a BeagleBone. He was a bit concerned about a few caps getting in the way of a board stack. This was tested by printing out a bit of plastic in the shape of the new board, adding header spacers and parts that might be troublesome.
While the idea is great, there’s not much in the way of a software solution or a toolchain to make plastic copies of completed boards. We know rendering 3D objects from KiCAD is rather easy, but there aren’t many tools available for those of us who are still stuck with Eagle. If you know of a way to print populated boards, drop a note in the comments.