That will read the codes. The black wire you are referencing is probably a ground wire. As I understand the system, the ecu gathers info from the cts and cam and crank sensor for ignition and injection timing. The ecu is a "black box" on all the diagrams I've seen, except for the first component on the ignition and injections circuits, which is a power transistor for switching those circuits ground path. It is good electrical practice, followed in the ecu, to control circuits with the ground path, as this carries less current than the power side due to resistance of the controlled components.

I'd start by following the fsm test series on the pertinent componenets. Cam sensor, crank sensor (a loosening crank bolt has been known to damage the crank sensor), power transistor, coil resistances. To test the coils, clamp the two coil plugs together with a hose clamp, ground them, supply 12v+ to the coil power supply, ground the coil ground wire, then break the ground, and both plugs should spark.