Can you see any discoloration anywhere on the components/board? If there is a short circuit or incorrect wiring, damage is often visible as discoloration as that smell is probably a component being fried. My guess would be that when you changed the wirings, it was wired incorrectly and that's caused damage to the autofire PCB (possibly permanent damage). It is unlikely to be an issue with wiring size because of the relatively low voltage/current involved going to the controls, unless perhaps you're using unusually small wires compared to the original wires (if the new wires are only half as thick that's a possible concern).
Doublecheck the wiring is correct - if not, you will need to correct it and see if the autofire PCB is still functioning.
Even if you think the wiring is correct, I'd suggest you try to rewire it the way it was before to see if that fixes the issue. That will determine if it was a wiring problem after all or component issue with something like the the connectors. If the PCB does not function after wiring it the way it was before, the PCB may now be damaged.
It's also possible it was wired correctly but a component happens to have failed on the PCB, but this is a highly unlikely coincidence.
Do you have a schematic for the autofire PCB? For reference, if your autofire is in fact damaged, it shouldn't be too hard to build a basic one:
http://ikotsu.blogspot.ca/2010/03/passi ... rcuit.html
