Question about compatibility between 4.0 V6 '06 and 4.0 V6 '08 wiring harness issues? Are there differences?

I have a 08 4.0 V6 and it looks like a motor was swapped to a 06 4.0 V6. Are the wire harnesses the same? Whoever did it has spliced wires at connectors all over the place in engine wiring. Are the connectors different to explain why they cut and put back together? When I bought car it had engine light on and it was in limp mode. I've replaced all sensors . I've replaced egr, throttle body, fuel regulator. I can start car. It idles good. I can drive at low RPM's around neighbor good. No issues. Once I try to eccelerate to drive on freeway. Check engine light comes on. Codes are p060b, p2104, p2110, p2111, p2135. I think I should replace chopped up mess with new harness. I don't know what's best to buy 08 or 06 harness. Anybody that has knowledge on this I could use some guidance. Thx in advance. Randy.
 
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