I have a 99 cavalier that I replaced the engine , because of a warped head the car would start with the old motor if you held the pedal to the floor and let out real slow, but it wouldnt start all the time . Now with the new motor is turning over the same way,like its not getting enough gas ,we had to use the old fuel rail because the plugs for the injectors were different could this be the problem?

if the problem is the exact same, i would start with the parts that are the exact same, like in your case, the fuel rail,

are there any other parts there were transferred?