Are you sure they're 3.31 cuss I've never heard of that ratio, regardless there's obviously something wrong inside, preload, mesh, depth, hell could be almost anything. Take it back to the person/shop that did the setup/install and have them fix it.
"Gear ratios available on the 8-3/4" axle through the years include: 2.76, 2.93, 3.23, 3.31, 3.55, 3.73, 3.91, 4.10, 4.56, 4.89, 5.17, 5.57. On OEM gear sets, the ratio is usually stamped on the ring gear edge."
I took the car to the guy who set up the rear, after hearing the noise he said it was a cracked tooth.