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To be clear it's a unit from autoxcooper and they are taking care of it properly and standing behind their product. I swapped the old unit that was noisy back on after inspecting the gears and pto, sealing the joins with permatex high tack sealant and refilling the oil. All seemed well with the gears, guess it's the rotor bearings that are making the racket. I did a boost leak test after swapping back on the old unit and found no leaks.
I messed up the logging after the swap to the old unit and only captured a short burst in 2nd. Blue line is rebuilt unit in 3rd gear and the red line is the old noisy unit in 2nd gear.
I will update once they get back to me with a diagnosis