I've had mine apart more times than I can count and don't worry about it. What are you supposed to do when you purchase a new crank and it doesn't come with a gear on it or the marks are gone on one or both parts I'm no expert but I belive the clutch gear is ballanced alone. As I said I have assembled mine different every time and never had any vibrations or any problems.
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1995 A kit TZ 250
1994 Rothmans NSR 300sp SOLD
1998 RM 250 freestyle/motorcross
1998 Meathanol burning CR 500 AF super retard/motorcross/sand dunes/play bike