Firing orders will affect wire separation. For example on mine 6 then 5 fire after each other so 7 and 8 wires are between them. Other firing order is 7 then 8 putting the 5 and 6 wires in the middle of the looms.

 

what RPM's does it give you problems? I don't know if i would believe that only 1 or 2 cylinders are misfiring. I say this because the 351w is a smooth motor, I have seen them run with 1 or 2 cylinders not firing at all and the only thing that points to a problem is the lack of power, the motor still ran very smooth.