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The Customizer guidance for the screw spacing has the correct value (71.5 for 80mm): "Typical values: 32.00 for 40mm fan, 40.00 for 50mm fan, 50.00 for 60mm fan, 61.5 for 70mm fan, 71.50 for 80mm fan, 105.00 for 120mm fan".
Also the screw holes should be 3.25mm by default for M3, that represents a 0.25mm clearance for the screw.
If you used the correct values for both of these parameters then check your printer calibration, for XYZ dimensions but also for extrusion steps/mm (the fact M3 holes do not fit makes me believe there is also an extruder calibration issue, since in that case the dimensional errors would be >10%). For XYZ dimensions I would recommend using an 100mm square calibration object (the 20mm cube is too small to reliably detect XYZ errors of 2%). For extruder make sure the diameter is still what you assumed it to be (you'll be surprised how many times manufacturers drift) and make sure accuracy is better than 0.5% (iow, if you tell it to extruder 100mm, it should extrude >99.5 and <100.5 measured). Always use large values, 100mm is better than 10mm in cases like these.