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Look in Fuel Sys / Diagnostics ECM45696 It may be what you are looking for.

Maybe try here: https://www.kinnettickreations.com/product-page/pcm-connector

After replacing the OPDA it's a good idea to chech the Camk Crank angle actual and learned values. You can dial it in using a decent scan tool and activate a relearn if needed.

The percentages that I quoted are from a log file done with HPTuners VCM Scanner. The actual voltages read with a digital multimeter at the TPS connector are 0.518v (10.36% of 5v) throttle at idle position and 3.948v (78.96% of 5v) with throttle at full, these voltages are with reference to the...

70% should be 3.5v Almost seems like a damaged Throttle body shaft.

What min. and max % values for Throttle Position (SAE) do you see with HP Tuners VCM Scanner? My 2006 is 11.4% at idle and 79% at full throttle.

Exhaust tubing is measured by its OD.

What is the part number of the spare PCM? This would help to identify if it is Jtec or Jtec+ Eg. 5604127AD The security system in the Jtec is called VATS VCM editor shows VATS for JTEC and for JTEC+ shows VATS and SKIM.

Looks like only a couple of the evap DTCs can be changed. P0455 and P0456

On the 2005/2006 TJs I believe you can but it would be illegal. The master DTC list of the pcm can be programmed/modified to disable the MIL/SES The tank would need to be modified or replaced. The flow management valve controls the venting of the tank during filling so removing it may cause some...

Flow Valve A.K.A. Flow management valve.

Check the cam sensor to crank sensor alignment. A sloppy OPDA and misalignment can cause long cranking at start up.

Same as yours. What about your channel settings when logging?

On 2005/6 models with the NGC3 PCM VSS is read to verify that the engine is no longer idling. It is used for torque management, idle rpm vs speed adder, power enrichment delay,

Here is mine in SAE%

Full throttle on my 2006 is just under 4.0volts. The PCM looks for the WOT voltage set at ECM44442 in the 2006 NGC3 PCM 3.7843 Volts

Not mine, a download from the tune repository. I just had a look at a 2009 file and it does not show the shift points. You may need to raise a ticket with HPtuners support. https://www.hptuners.com/help/VCM-Editor/Content/Contacting_HP_Tuners.htm

If you share your HPT file at the HPtuners forum someone can check it over. I don't think you can share it here.

Make sure that you are using advanced view, it is under the EDIT dropdown.