Assembling an FPGA board on 2 layers PCB

If you put a lot of care and work into the design layout you could get it working on a 2 layer PCB (I'm going to catch a lot of flak for saying this).

But at the price of 4-layer boards nowadays I would use a 4-layer design. It will make life easy, especially as you are receiving data at a 100 MHz rate from an ADC. Do not forget that all those fast outputs need well terminated/designed transmission lines unless the distance traveled is less than 15 mm (what you will not be able to achieve on a 2-layer board).