- if I short the wires, the auto focus triggers. Which means that the cables are all good.This is why I'm confused. Everything seems to be good. The only reason, that I can see, for the auto focus not triggering is that the resistance between pins 4 and 5 on the 4N25 only drops to 100 ohms. It doesn't drop to zero.
Do you have a wired shutter release? Does it work to trigger the camera? On some cameras you might have to enable the shutter release via camera option.
Did you see the comment from Michael about Arduino pin 13 being unsuitable because of the on-board LED and resistor which are connected to that pin? Did you try with a different pin?
I think the problem was with the 4N25's, not the D13 pin