The PDF didn't print properly for me. It appears to be the same size as the Word attempt I made. Drill holes for the components don't fit properly. It's easiest to test against the 40P as it's the longest component on the board so a little deviation in dimensions are obvious once you line up the first pin and the last pin overshoots the hole completely.
Note my results could be due to printer drivers or other issues. But I'm doubtful. I guess if I had some verifiable test images to print to confirm my printer wasn't mangling the sizes that would eliminate my printer as the issue VS any of the images, methods of resizing, or files provided.
If you don't yet have board components you can use a spare IDE cable to help gauge the 40P connector holes on your prints. It's not as good as the actual connector pins which are much obvious visually but you should be able to see if they are dead on or not with the ribbon cable or if they are skewed slightly.