BOUGHT USED MOTOR BUT INTAKE MANIFOLD IS DIFFERENT ARE THEY COMPATIBLE

Your engine's computer module will not be compatible with the new intake. You may be able to update it but more likely you will have to replace it with the one compatible for the replacement engine - assuming even that can be plugged into the existing wire harness - if not, then you have to replace the wire harness or make one compatible, because chances are some sensors aren't going to be the same. This is why when you replace an engine it has to be 100% compatible with what you already have, or you end up replacing a lot more then just an engine.