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We have some detailed suggestions for minimizing the difference between the positions of different pen tips, in our documentation here:
You should be able to get consistent alignment by using procedures like these. (It may not be exactly the same position — for example if you’re using different pen types, but the differences should be consistent.)
If you know how much to shift, one thing that you can do is to use the “walk” commands in the Manual tab of AxiDraw Control. Movements made there can be used to compensate for changes in pen position. You can also potentially shift the graphics on one or more layers of your drawing.