Are your gears stock from Ford?I just installed full suspension on my 2016 GT including steeda springs, shocks, and struts, and the BMR bread and butter rear suspension package which includes the BK051 bushings. It says directly on the BMR site that this part will increase NVH. I too notice a slight whining noise from the Diff now. I have 3.55 rear gears BTW. Not sure if going to a different gear like 3.31 would help any or not. For me it is slightly annoying but its not to the point of being intolerable.
YesAre your gears stock from Ford?