autobody

Hello everyone this is my first post so please bare with me. So I dropped a 6.0 in a wrangler now won't run right. So my story starts with buying a 5.3 with a dbc I bought a standalone wiring harness for a 5.3 and all the goodies to do the swap. So long story short the 5.3 ordered had at least 3 weeks before I could get it I was impatient and found a 6.0 local in my town and picked it up the next day. So dropped it in my wrangler. The guy who I bought the stand alone harness from told me it is the same harness so I proceed to install and everything seems OK. Got the all the sensors hooked up minus the o2 need the exhaust put on first. So got this thing fired up open headers and no o2 sensors the thing is a animal spins 35s first and second gear (Turbo 350) so off to the exhaust shop got the exhaust made and bungs welded in for o2 come to find the 6.0 oxygen sensors won't fit into wiring harness? So I returned them and found the 5.3 oxygen sensors worked perfect with the harness. So I left the muffler shop and this thing is a total dog.? I wonder if the oxygen sensors are affecting anything? Btw 3 inch exhaust and flowmaster. I also had a code for a knock sensor which I know can affect performance I changed both knock sensors with new and cleared code and still have no power. I just don't know if the wiring harness is different between either motor? Help please!