Hi, I'm fairly well involved in the Proxmark community and have looked into the Proxmark design in depth. I am currently in the process of redesigning it with slightly more updated hardware, the
latest working prototype uses the same FPGA as your LA, an XC3S250E 100VQFP, and ADC08060 A/D amongst other changes.
The FPGA currently coded in verilog does the basic 14443 a and b RFID demodulation, however the rest of the protocol is handled in software on the ARM microcontroller (AT91SAM7 based). The good news is that the existing verilog code is trivial to port from the original proxmark Spartan2 FPGA to the new Spartan3 and I have in fact tested that it works in practice. The not so good news is that you need to either implement the further higher level protocol handling in the FPGA or add an external microcontroller (or maybe look at an FPGA soft core micro).
Since that video above was shot, the board was redesigned several times and the latest one should sport a touch pannel 320x240 LCD which remains to be tested, as it is attached to the FPGA pins and I have yet to write the verilog code to drive it.