How are you measuring the PDF? Since you would need to plot the PDF to accurately measure the PDF, is that scaled correctly? PDFs try to force a Fit to Page IIRC.
Illustrator is not the most accurate at measuring, either. How does the drawing look when Exported in other Vector Formats? Illustrator can import dwg and dxf.
I have zero problems using 3D in AutoCAD, including sending accurate 2D files to a WaterJet, Plasma, etc.
A drawing and sample file would help.