340 Not firing on all cylinders

Not being able to see what you have in detail, it's difficult to guess, but refer back to the diagram.

The neg side of the coil should only have 1 wire, unless you have a tach, and if so, the tach wire hooks there as well

The POS side of the coil MAY have the ballast bypass hooked there. Once again look at the diagram. ORIGINALLY the brown bypass wire coming out of the bulkhead connector hooked to the coil + side of the ballast resistor, so that is the "same thing" as the plus side of the coil.