The green plugs are for diagnostics use only.. leave them unplugged. The CEL is supposed to blink when they're connected.
To reset the ECU, just unplug the battery, step on the brake pedal and reconnect the battery after a few minutes.
As long as your speedometer is working, I'd chalk the codes up to plugging the diagnostic connectors in. See what codes you get after you've reset the battery and left the green plugs disconnected.