Alright, I did get SPI working with my shield. I had to wire the pins to the ICSP pins since I was using a shield-shield and those pins aren't set.
Anyways, with this configuration I could get your library to work in SPI mode but only when PN532_HW_SPI was set to 0.
When I was using hardware mode it was failing on the ACK when writing the command to get the firmware.
I'm getting - 0x0 0x0 0xFE 0x0 0xFE 0x0
It should be - 0x0 0x0 0xFF 0x0 0xFF 0x0
Are you using the hardware mode with SPI? Could this be an issue with my hardware? Any ideas on how to proceed using hardware mode?