Motor Swap Help

So I have been helping a friend ,fellow TW member on here, doing a motor swap on his truck. He had a 02 tacoma prerunner 2wd automatic 2.7 4 cylinder motor. He decided that he was going to keep the truck no matter what and put the 3.4 v6 motor in it. Through all the problems. Currently the old motor is out and the new motor is in ,bolted in with new motor and trans mounts roughly near stock 4 cylinder position is or more forward.
He has most of the parts he got
02 3.4 tacoma motor and transmission. Starter, alternator, ps pump., air intake and maf.. etc..
He got a 02 3.4 automatic 4WD engine wiring harness, this is where we are not sure how to install will it be all plug in to the motor and then??? Or will we have to modify it?
He also has the v6 2wd and 4wd ECU. And he also got the battery harness, and v6 fuse box . The engine harness and 2wd v6 ecu is already put in the glove box and through fire wall.
Any help is useful thanks.