Mega is overkill - something in '1284 familywill do 32 IO and exist already in small form factor.
Scroll down to 3rd board here
Cross Roads Electronics Can send you a bare board for $3. Build up as you need. Connect an FTDI Basic or FTDI Cable to download a sketch after bootloading, or just program via ICSP & skip bootloader.
Can assemble with right angle connectors & easily plug on crimp terminated wires from pololu.com
I/O pin & ground located around the whole board.
Examples
http://www.pololu.com/catalog/product/1906
Pololu - Wires with Pre-Crimped Terminals 20-Piece 10-Color Assortment F-F 36"
pick a width for the # of pins used - maybe just 2 pins ever to go off to each wiring seciton.