??
I'm not sure of the issue you're talking about - you have the dyno coil mounted on your bike something like this, right ?
In the photo, the "dangling" bit is the ICU or ICM (Ignition control unit or module). I've got room to run the plug wires to the left or right cylinder either just behind or just ahead of the wires that go into the ICU. It doesn't matter if you put the left cylinder plug lead into the "front" or "back" position on the coil - both plugs get a spark at the same time (wasted spark ignition system), so you can do whatever works best for plug wire routing.
while you are in there, if it hasn't been done for a few years, it would also be wise to unbolt the ICU from its aluminum alloy heatsink (you might have to tap or pry them apart GENTLY if it has been a REALLY long time) and clean the mating surfaces with some emery cloth - you want clean shiny metal without deep scratches. Apply a thin schmear of heatsink paste (can get at Radio Shack or other electronics hobby shops) to the metal back of the ICU and bolt it back to its heatsink and back onto the bracket on the frame.
