2000 Civic EX Swap help

Ok heres whats going on. I recently swapped a 2001 GSR engine into a 2000 civic. The problem is when i use the EX ecu it starts, but when i use the GSR ecu it doesnt. I was told by hasports that it was because the 2001 GSR has the imobilizer system on it. Im using a wire harness from a 99 or 00 civic SI. Could it be possible for me to just use like a 96-99 GSR ecu? Ive been told by some i can and by some i cant...