Yeah - the ECU thing bugged the hell out of me.
My initial thought was the same as your's, the engine is just a hunk of metal that a computer tells what to do, and as the 00-04's all have the same engine, it should not matter what ECU, other than for manual or automatic, 4wd/2wd, 4 cyl or V6, etc.
Nissan told me no, the SENSORS on the engine that TELL THE ECU what's going on have different resistance ranges and so forth, and if I use my '01 ECU on the '03 engine, it would throw codes at me all the time, or not even run.
So, I baked the old one in the oven in case I might need it...but ordered the new one for a manual '03 V6...and will drop that one in.
I MIGHT try to use the '01 ECU first, just to see if it works or not, as I'm into the experimenting thing...if I have the time.

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- TJ
2001 Xterra '03 VG33, SE 5 spd, 305/70/16's, Revolvers, UBSkidderz, Doubled AAL's, 3"SL/2"BL, winch/bumpers, skids, sliders, OBA, Snorkel, pine stripes....
Friends don't let friends drive stock.
http://www.gifsoup.com/view/501230/tj-tackling-crawlers-ridge-o.gif