Just to sketch it a bit. It is not possible to stack the midi shield on the miniAtmegatron or vice versa. Also they may not be pin compatible (to be honest, I did not check all of them - for Rx and Tx it is ok). What I did:
* instead of the usual headers, I stuffed the miniAtmegatron with stackable headers. It is just fine, they are not blocking buttons or pots. These headers allow me to easily hook up jumper wires.
* put the miniAtmegatron on the Arduino board
* put the midi shield next to the Arduino-minitAtmage combo
* using jump wires, connect the 5V, ground, Rx and Tx between them
There you go...
* instead of the usual headers, I stuffed the miniAtmegatron with stackable headers. It is just fine, they are not blocking buttons or pots. These headers allow me to easily hook up jumper wires.
* put the miniAtmegatron on the Arduino board
* put the midi shield next to the Arduino-minitAtmage combo
* using jump wires, connect the 5V, ground, Rx and Tx between them
There you go...