Since I was there and looked into some of these, answers below:
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1) For the V6 airbox swap, is 2002 my only option, or can I use the airbox lower half and intake pipe from other years?
2002 and 2003 V6 airboxes look to be identical. I snagged one from a 2002 since it was the only one with all of the mounting studs still intact. There were no other years for me to compare with, but those two appear to be usable.
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2) Assuming I can find one with skidplates, what will and won't interchange with an '05 CRD? I'm mostly concerned about the fuel tank skidplate, but would like to know about any issues I may need to look out for (especially fiddly things like, "be sure to grab the nutserts from...")
None of them had skidplates, so am still in the dark on that one.
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3) Does a V6 with the tow package use the same mechanical fan shroud as the CRD? In upgrading the fan and clutch on ours, I found that the previous owner's modification to the fan shroud was a lot more hackish than I would have preferred, and would like to have a 'clean' one to modify.
Short answer: it doesn't appear to. The top tab on the CRD shroud is much deeper to account for the additional depth of the A/C condenser, intercooler, and radiator being in a stack. However, it may be possible to use the lower half to repair a CRD fan shroud that was improperly cut. This needs further investigation, though.