Build the 4.6 or 5.4?

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djljr

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Planning to buy a used engine, either a 4.6 or 5.4 and have the engine rebuilt, blue printed, some torque cams and headwork. Are there any sysem issue that would prevent dropping a re-built 5.4 into my '03 to replace the current 4.6? Like ECM issues (I know I would need a tune) but I wouldn't go the 5.4 route if the replacement was not a straight forward bolt in.
 
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