Adapting the Eagle file to your needs is really not to hard, I did that, too. Just download the boards you need from ucapps.de, load them into Eagle and copy all stuff to one board. From there on you only have to connect all the supply lines (5V, GND and signal lines) correspondingly and start wiring up everything.
It´s a work of quite some hours to do bigger projects, but normally it´s worth it.
The only point is that perhaps some people did that, but it´s always a highly project-specific solution, so *normally* you will not be able to use it straight-forward.
Just as an suggestion. Greetz!
PS: Nope, I did *not* connect IDE cables as I only had to bring the signals to the board in the end (pots, encs, AINs, DINs and DOUTs integrated in one BIG stripboard).