Yep definately sounds like something amiss.
Think you have start all over from beginning by checking wiring is correct from ls harness to car...then check if correct cas (2 types) for engine/pcm.
After that you'd be questioning pcm or tune with vats is actually off ( yes again)
What model is pcm & engine/harness from? All from same donor car or mix n match parts?
Did dude who did harness conversion also put in obd2 port so you can use scan for faults or get it tuned?
Post up a pcm wiring diagram then go from there.