1- both are the same. there is another board that altium offers and it is called the nanoboard. the altium livedesign evaluation kit is for evaluating the altium design software.
2- there are a number of different spartan 3 variants; XC3S50, XC3S200, XC3S400, XC3S1000, XC3S1500, XC3S2000, XC3S4000, XC3S5000 and they have gates from 50,000 (XC3S50) upto 5,000,000 (XC3S5000). now with that much gates you can do anything!!!
3- Protel DXP 2004 is a PCB design software and Altium Designer 6 is a complete suite of FPGA-PCB softwares. the previous version of Altium Designer 6 was the Altium DXP 2004 which included Protel and Nexar (the FPGA design software of altium)
4- i use the Altium DXP 2004 with an 800MHz and 256MB RAM system and it works fine. but the higher the system specs the better because PAR takes alot of time.
5- the board doesnt have a USB connector but you can make your own USB connector board and interface it with the Altium kit.
i hope that helps