just so were on the same page, youre dropping an 01 motor into an 04 chassis? youre also utilizing all the sensors/parts from the 04 motor correct? the 04 drive-by-wire would need specific part#s for pedal/tb/ecu/etc so hopefully youre reusing all the 04 parts on your 01 motor. in 2002 was a big changing point for all the electronics, but your changing the motor alone, this should workout. also, by saying it runs on 'ether', im assuming your spraying it down the manifold, and not over the maf or tps sensors?
if youre not getting fuel, youll need to chase some wires, assuming youve already T the fuel line and know theres no fuel pressure. the cam and crank sensors can prevent fuel, hopefully you did solder your wires for the cam sensor, as crimp-ons usually lose voltage or have intermittent connections which will mess up the ecu when its trying to time the motor. you should check your fuses as well, maybe you popped a fuse and didnt hear it? also, nats can prevent fuel on startup if nats is armed or the fuses/relays are dead, assuming you got the motor in and it is turning itself over?
lastly, assuming youre using all the 04 parts, you may also need to do all 3 relearn procedures (pedal released, throttle plate, idle relearns), however none of these usually prevent fuel.
EDIT: did you get any ses codes? you can also follow the troubleshooting in the fsm, hopefully you didnt miss something.