Gear will whine if they donâ??t mesh perfectly. If a gear set is not cut as a set, it will make noise. Improper installation., too much or too little backlash or improper centre distance spacing can make gears â??singâ? a little too. Tooth design and cross sectional profile shape will also make gears whine. Herring bone cut gears are always loud, straight cut gears are loud too. Sometimes this is necessary to make a gear set strong. I think, in your case, this is either installation error or more likely manufacturer error of the gear set.
If this noise was there after install, you should have taken the car back to the shop and complained.
Also, sometimes damaged or worn out bearings can make noises like this too. If the bearings were damaged during the swap, the noise would make sense.
I hope this helps.