U should note your rapid prototype's target, it's for source code verification, module emulater , functional test or system estimated.
If you just target the first one, U should not change the source code. But just replace the ASIC special IP, such as PLL or Analog part. Another, you should regenerate the memory EDN netlist for FPGA version. But the control logic of memory as the same.
One important thing, FPGA can't run speed as ASIC. Some times U should use low speed clock.
Another, U should care how many clock domain in your design, and constraint them carefully, if you want a excellent design.
Xilinx device limit: too few BufG
Added after 21 minutes:
please ref