Uno or Mega, the pin connectors are all 0.1" spacing. On one side there is a 0.1" gap between set of analog pins and other pins. On other side, they all are digital pins but there is a 0.05" gap between the 2 sets of connector.
Did anyone ever explain why the different gap spacing? And is 0.05" right? It seems odd to me.
I am trying to make ISP shield for 8535/84/164/324/644/1284 MCU that uses 40 pin DIP. I've used them a few times and I am tired of hand wiring them on breadboard to burn bootloader. It'd join my family of '328 (28 pin DIP) shield, ATTiny 45/85 shield, and ATTiny 24/44/84 shield.
it also works as a key, To help keep people from connecting the shields in the wrong way.
The pin spacing on the Analog side of the board is .1", This includes the spacing between the analog and power headers. The pin spacing on the digital side of the board between the 8 and 10 pin header is .15". your measuring the distance between the plastic portion of the headers, not the center of the pins.
There's another way to check the pin alignment is correct. I have Adafruit library that has Uno form factor. I added it temporarily and moved that over the existing board layout to verify pins are all correctly lined. Then deleted the temporary Uno board.