No, you got it right. The 18 AWG BLACK wire actually looks bigger than the 16 AWG wire, because it has thicker insulation.
The wires are paired because when they are used for the WOT Box, they both go to the same splice point at the ignition coil power.
In this installation, the red of the pair provides power and the black of the pair powers the solenoid. The single black wire goes to ground.
there are pictures here:
N2MB Electronic boost controller installation guide
