Check engine light on a 94 Camry

I have just replaced the motor of my 94 camry's 5sfe engine with a 3sfe engine. Car runs fine except I have a check engine light come on twice when im in the same area but it doesnt come on any where else on the road. I have check the oil, transmission, gear box, power steering and radiator levels and they r all within what the book calls for, but I can not seem to figure out why this check engine light keeps coming on. Can someone help me plz?