Here is a draft shield schematic:
Each of the I2C devices work with 3.3V (DS1307 is 5V, but the I2C bus is open collector and it supports 3.3V comms) so there is no level shifting required here.
The PN512 won't be on the prototype board here since it is located on the NFC Explore, but it is here to map out used pins. In the final version, it will be completely integrated with the shield. Note that the pins not required by the NFC Explore board will only go to the prototype board underneath and will be trimmed (the NFC board will sit on top).
The extra GPIO pins here are buffered using the well known BSS138 to 5V. The 5V value for individual I/O can be swapped for any other voltage as requred. This also provides protection to the pins.
More to come tomorrow.