2 sided milling question

Anyone out there, I have a question regarding 2 sided milling. I cutting a Telecaster style guitar neck. I’m placing the neck on a 3/4 piece of MDF 6” wide 32” long with a center line drawn a the MDF The neck blank is 4.0” wide, 30” long The neck blank also has a center line drawn onto it. Then I drill 4, 1/4” holes into the corners of the neck blank into the MDF the insert 4, 1/4 machined pins into the holes. After cutting Side A, when flipping to cut side B the center lines do not line up. I have also tried 2 pins on the center line on opposite ends still lines do not line up, anyone have an answer I would greatly appreciate. I completed the cuts but by visualizing the track cut in the MDF left by the side A contour.

@Dan5450, if you use four registration holes, they need to very accurately/symmetrically straddle the axis of flipping. If you use two holes along the centerline, they need to be very accurately on the axis of flipping. Any off-symmetry will be doubled in your side-to-side misalignment. For the holes-on-the-centerline situation, a thing I have done in the past is to use jogging/MDI moves to drill the holes in the already-placed rawstock and down into the spoilboard. Given your geometry is centered in Y along that axis, your side-to-side alignment should be well nigh perfect…

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