One thing I don't think most people realize (or can utilize) about that template is that the PDF still has the capability to be edited by Adobe Illustrator. According to Illustrator, the crosshairs for drilling holes are 1.62" apart horizontally and 1.485" vertically. The joystick hole's center is 4.903" horizontally from the center of the first button. The vertical center falls just below the top set of button holes. It's about 1/8" higher than being actually centered with the buttons.
Obviously, if you're going to use this template for drilling, you'd want to just print it out at 100%. The type is in a different font, but this template is identical to the drilling template printed in my X-Men vs. Street Fighter manual.
I measured a lot of cabinets I found, and tried to find a good compromise between Capcom's layout and the Neo-Geo MVS layout. Attached is my final drilling template. The 7th button, while at an angle, is the same spacing as the six buttons' horizontal spacing (1.62" from the bottom left button). This puts the 7th button pretty close to the joystick, but this placement is very close to the real MVS cabinets.