OK so MAF is working fine, I stripped everything back, removed the TB and rechecked marks. All ok so I am 95% sure the TB alignment is correct.
Where I should have started is looking closer at the Airbox sensor. While I thought it was fine, have a look at the image below.
Can anyone assist with the part number? Mine has rubbed off, and my google fu is letting me down. A photo of your sensor located in on the airbox will be brilliant if anyone can assist.
edit * ep-9451-r3a does look like a part number of sorts... Now Found Jeep # K56044591AA
Ambient temp in Torque is listing 0 degrees C...
Will leave Timing belt exposed until this is solved though.