Jeep jk 5.7 hemi, 65rfe swap

[Hemi jeeper]

Hello everyone,
I have something strange happening.

My car is a 5.7 hemi vvt, 65rfe swapped Jeep JK (2012 both jeep , engine and trans). I have a jk 3.8 restyiling shifter (prnd12). It works great in D but as you shift into the manual positions (1,2) after a few gear changes it goes to limp mode.
I see on HP tuner that it does not recognise manual shifter positions as 1st or 2nd gear but as a coordinate such as "unknown 48". I was wondering if that was the issue.
Some more information that may be useful, wiring harness is from hotwire (5.7 hemi-545rfe) and transmission has been completely rebuilt.
The car has worked great even in 1,2 positions since i bought it but after some ecm issues i had to buy a new one and here we are

Does somebody have any ideas?
I attached the two tune file.

Edit: I wanted to try to write the old tune but it says that IDs are different

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the 545rfe is a 5 speed and the 65rfe is a 6 speed i would get a pinout i believe you can probably move a wire around and straighten it up