Using Trinity Diagnostics for correct 02 sensors wiring

[chris bjurman]

I Have 2006 dodge charger srt8 with long tube headers, I'm using the trinity V.1R13k. I did some work under the car and using the diagnostic to show trouble codes for connecting the right O2 sensors to the wiring harness. I disconnected all the sensors and extension harness. I installed one bank 2 sensor 1 passenger side pre cat. turn key to run not starting the car, using trinity to show trouble codes. I get the other three O2 sensors showing not connected like it should. so I keep doing this one by one clearing the codes each time and cycle power on and off.
bank 1 sensor 1 is drivers side pre cat.
bank 1 sensor 2 is drivers side post cat.
bank 2 sensor 1 is passenger side pre cat
bank 2 sensor 2 is passenger side post cat.
So all connected, trinity not showing any trouble codes. I start the car and drive it. then I get P1128 upstream HO2S sensor swapped see P0040. P1129 Downstream HO2S sensor swapped see P0041. P2016 Intake Manifold runner position sensor/switch circuit low bank 1. the P2016 I don't have that sensor so I don't know why it is showing it.
I then go back through the trinity again using the trouble shooting and keep ending up with the wires going to the sensors it was before with no trouble codes showing. start it again and drive and keep getting the p1128,p1129. I have swapped Bank 1 downstream with upstream. car runs rough but I don't get the codes of sensor swap.
Bank 1 and Bank 2 pre cat new Mopar sensor 56028994AB
Bank 1 sensor 2 new Mopar sensor 56029049AA
Bank 2 sensor 2 new Mopar sensor 56029050AA
New MAP Mopar sensor.
So I'm thinking either the trouble shooting is wrong or the way it determines sensor swapped is wrong. Any advice on what to trust? How does it show they are connect but then can determine upstream and downstream is swapped? Thanks Chris