Ah, yes. I remember when I ran into the EXACT same issue as you when installing mine. For me though, I had to keep changing harnesses around until I got no check engine codes. I do not advise you do the same.
There will be a long skinny heater hose provided with the 2J Intake. You must connect that to the right side of the intake and route the hose around the back of the engine leading up to the front of the engine between the intake manifold and the battery. There will also be a small silver sleeve provided with the kit. Put that piece into the tube and connect one end of the adapter harness into it. The other two ends connect near the intercooler piping and where your intake used to be.
I can provide pictures later in the day if need be.