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Well, it's very odd that the intake cam was not also out of alignment. Something else is amiss. Finding the optimal spline gear will give max cam advance when Vanos is fully engaged, but I don't believe it will affect cam alignment.
Assuming you're using the Beisan kit and procedure, I would say read back through it and see if you omitted a step or misunderstood a step. If you still can't figure it out, call Beisan. I've talked to him before and he's very willing to give advise.
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