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I simply put the 2 halves on top of each other and drill straight through with a drill press. Only then do I start shaping them. Drilling them separately is a bad idea unless you have identical scales and you use some sort of tool rest to line them up identically.
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The reason I avoid drilling before shaping is that it there can be some error while shaping which would cause the pins to be off center, or even just that it would look better in a different place after the shaping.
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So here is what was up with the Boker:
1: The Original scale was slightly warped, almost discernable.
2. The wedge was too thin to flare out the scales enough to overcome the warping. I made another wedge, slightly thicker, with a bit more of an angle to it.
3. Tightening the pin in the front first was key to getting it to center properly.
Thanks for all the recommendations and ideas.