I started from the original Mega files and removed all unnecessary parts, keeping only the board size and header pads.
Start from there and add your own parts.
http://dl.dropbox.com/u/2669959/Arduino%20MEGA%20blank%20shield.brd
The SCH still needs some cleaning !
If you have better files, post them in this thread...
http://dl.dropbox.com/u/2669959/Arduino%20MEGA%20blank%20shield.sch