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Unfortunately I don't have a lot of information on your vehicle, however, assuming the wiring and pin outs are the same, If you didn't have the 4.6 ecu coded into the immobiliser after the swop then the vehicle security systems wouldn't let it start as the whole system has to be 'matched'.
Options I see are getting the correct ecu (and if necessary wiring loom) fitted and programmed into the vehicle, or getting the 5.4 ecu custom remapped on a rolling road.
If, you have a local ecu repair specialist, that can disable the immobiliser on the 4.6 ecu this may help, but is not advised for security reasons.
Some ecu repair centre's have tools that can read the content of the memory chips on the ecu, decode the immobiliser data and then rewrite back to the ecu with the immobiliser bypassed.
This isn't a diy process unfortunately, often involves some soldering of pins and jumpers and needs dedicated equipment and computers.
Likewise, a good centre may be able to read the fuel mapping off one ecu and program it into the other.
I am in the UK and unable to advise you of any local centres unfortunately.
Did you have the 4.6 ecu coded into the immobiliser or just plug it in and try?