Hi! Read the install instruction, a first check engine right after install is normal and expected. Clear everything by itself and everything should be fine.
Your serial end on the harness is unused in your case, it's for Rev 2 and Rev 2.5 unit. Your rev 3 uses the included USB cable.
The small two pins is for meth kit connection. Your next purchase
Enjoy your car now
What octane are you using? And what other mods you have?