The instructions are definitely confusing, but if using a PerTronix-I Ignitor module, you must run the resistor to the coil, and no resistor to the module. The coil does not determine the need for the resistor - the module does.
If the coil is laying on it's side, that can cause early failure, as the cooling oil in the coil can have an air bubble that exposes the top of the core windings. Install upright whenever possible. However, I don't think that is the big problem here.
That is the part that determines if a resistor or ballast is used or not. If you do not want to use a resistor or ballast to the coil, then you must get a P-II or P-III module.
Dan is again correct. I found where we went through and tried to explain this more than a year ago in this thread? What made you decide to change it?
David