Armando -
RE: the pins ASK/OOK, MOD and SYS_CLK...
SYS_CLK is (as you said) a divided output in the event that the system needs a reduced BOM (using one crystal) instead of two (one for TRF, one for the MCU) - this is also handy for ensuring the MCU and the TRF are syncronized 100%, too as we have shown is useful for card sniffing function in this application note ==> http://www.ti.com/litv/pdf/sloa184
MOD pin is used in one of two ways - either as an input when in Direct Mode 0 (AFE mode) to directly modulate the carrier with MCU GPIO (useful for non-ISO standard card operations, as seen with Mifare Classic devices) or as an output when developing so you can see the subcarrier output of the receivers directly...see register 0x1A bit definition in the data sheet)
ASK/OOK pin can also be an input (to feed a subcarrier in directly, to test out the decoders).
For card emulation, these last pins can just be pulled low through a 1k resistor or connected to an MCU, as shown in the references.