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it could be the relay but if the crank sensor is not working you wouldn't have power to fuse because this tells the pump to turn on and activities the spark so if you are missing both of these then it i the crank sensor.
so if I understand you just replaced motor and it will not start correct? and you have no fuel or spark?
relay is usually gray on bottom left in panel under steering column. here is part #8533176. They use this relay for alot of different applications.
the relay is the only thing left you have replaced the pump and igntion switch the relay is it. codes do not need to be cleared.