This motor has two direct fire ignition coils (which do not use plug wires on the plugs that are directly under the coils, but each of those coils also has a connector for a plug wire that goes to one of the other cylinders); and two plug wires which connect from the coils to the two cylinders that do not have coils above them. The two center cylinders (#2 and 3) have a coil on one of those cylinders, and the plug wire from that coil connected to the spark plug in the other center cylinder. The two end cylinders (#1 and #4) also have a coil on one of those cylinders, and a plug wire from that coil to the plug in the other end cylinder.
Here is a link to a photo of the coil, showing the connector for the plug wire: (http://www.rockauto.com/catalog/moreinf
And here is a link to a photo of the plug wires: (http://www.rockauto.com/catalog/moreinf
From looking at the photos of the coils and the plug wires; you should be able to see which wires to change, and from my text; you should now know where the wires should go.
I hope you realize that the spark plugs in this motor are intended to have the electrode gap adjusted to a much smaller distance than the plugs in most other engines. These plugs should have the gap set to .028" (0.7mm). Most plugs these days are set to .044" (1.1mm). Contrary to popular myth; spark plugs do not all come preset for your motor. Many plugs fit several different motors; which often use different gaps. If the plugs in your motor have been incorrectly gapped, or are an unsuitable choice; it would cause misfiring.
This motor should only use Double Platinum or Iridium plugs. I would recommend Autolite # XP3923 or Champion # 9801 Iridium plugs for optimum performance.