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"Subtle differences" is the right term here. I would expect needing the upper intake plenum and electric throttle body. I would expect wanting the lower intake plenum as the 01-02 were prone to have loose power valve screws, unlike the 03-04...not that you can put some thread locker on them. (Speaking of which, you should tear down that 02 intake to confirm all power valves AND screws are present and not loose, in case that engine was pulled for some other reason). You'll want to check the camshaft position sensors between both engines. When I was last pulling parts from the junkyard, I want to say the sensors are different and in different positions, not to mention I think there's on less sensor or sensor hole on the newer engines. I'm forgetting a detail here, but probably easily to resolve. I think beyond those items, there isn't really all that much else?

I don't know the VQ, but I'm told a bunch of stuff changed between '01/'02 and '03/'04, enough that it may be less work to track down a later donor than to get what I'm assuming is a cable-throttle engine working in a drive-by-wire truck. (I don't know offhand when that changeover happened--if it was mid '02, and the donor was late '02, you may be in better shape than I'm assuming here.) I use the parts lookup on nissanpartsdeal a lot to work out when parts were used. Might help with working out part compatibility. CamperDan mentioned the cam phasers--look those up for '02 and '04 and see if it's the same PN. As usual I'll plug the factory service manuals. Free download from Nicoclub. EM and EC sections will come in real handy for this. There's some good info in there if you can wade through all the hand-holding for using special scan tools that you don't have. And yes, do take a bunch of pictures, both for your own reference and to help the next guy who asks the same question.