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I have a similar alinement problem. I've talked to Mike Pierce and he has corrected a number of these carbs. He makes a rivet to fit the bad hole. The head prevents it from getting into the engine. Then he uses a (guide/bushing) to drill a new hole. It can be clocked to the correct position for drilling. I think you could leave one bottom hole. Plug the other bottom and top hole. Then drill new center and top holes away from the old holes. I would only be concerned about the horizontal lines of the holes, not the vertical lines.
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Tom
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