The generator gear is actually 2 gears separated by some kind of rubber pre-load offset. One gear has to be rotated slightly relative to the other, so that both gears will slide on to the clutch gear.
I did the 04-05 swap and this replacement was the biggest PITA EVER!
Like I posted once before, there is probably a right way to do this, but the way I did it must have been the wrong way. Like building a ship in a bottle, only with bloody knuckles! In retrospect, maybe it would have been easier if I had removed the clutch...
To answer the question, I don't know how critical it is to match the gears. I threw mine in and it worked.
TIP: when tightening the generator cover screws, do so a bit at a time and make sure you can still turn the crankshaft. The first time, my gears didn't match up right, and after I tightened the screws, my engine would not turn at all! Scary!