What about connection of HT leads into the double coil?
HT leads into plug caps?
Try swapping centre spark plug with one of the outers just for shits and giggles.
As stated above, if you swap wires from Ignitech box to the single coil for the same to the double coil does the double coil spark?
Issue with the pick up or wires from it to the black box?
Issues with wires from black box to coils?
Check/confirm connections that you might think are beyond obvious, you never know.
Wiggle wires as the engine is running on one cylinder. If it even attempts to fire the other cylinders then there's your fault.