Most likely tune related. I would swap over to an Ecutek tune and tell your tuner to input in the upgraded diff data.
Source: I tune cars with different gears all the time, my 09 auto has a 3.9 diff ratio.
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Creator of the GTR TT Conversion Kit, NA Record Holder (401WHP)
Ecutek Master Tuner (VQ37, VR30, VR38, B58, S55, S58)
BTWTuning
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