Not all 100 pins of ATMega 2560 are used in arduino mega

You could also use something like the Mega2560-CORE by Inhaos datasheet,
that has a lot more pins broken out. I'm not shure if they left some out, check yourself.

Mini2560-1.jpg

The have a nice protype board for that modul also (with 4.096V precision voltage reference).

EX-2560LT-2.jpg