Going from a 2V to a 3V is going to be a nightmare. Completely different harness/engine controls. You are going to have a wiring mess for sure. I'd stick with a 2V 5.4L just because it's basically a bolt in with some minor ECM changes. That is unless you're just itching for a good, level 4 difficulty project.
I'm not saying it can't be done, but because the engine controls on the 3V are so integrated into the rest of the vehicle, you're likely to find that even if you got the engine to run, many other subsystems are going to have issues because of the incompatibility between communications protocols. 2003 and earlier use SCP/J1850 communications and 2004 and later use CAN communications.
Take care.
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Bill Cohron - The Mad Doctor  
Power Hungry Performance - The ORIGINAL in Ford performance tuning... Since 1996!
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