Hey Brent,
did you check your machine for rectangularity (squareness)?
For alignment of two-sided projects it is good to work with wood dowels in the wasteboard that fit into holes that go through the workpiece, or through a helper frame on which the workpiece is attached. A good video that shows this technique is this video.
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Here you see milling the reference holes on the 1st workpiece, top side
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Note that when flipping over the workpiece, if the four reference holes don’t fit, your machine is not square and you got to adjust its rectangularity (squareness).