Rear end clicking
There's also gears in the differential unit itself, not just the ring and pinion gear that previous owner had replaced...
You need to get under the car with no load on the driveshaft, ie. trans in neutral, to be able to move the joints enough to see a problem.
You probably have a bent axle flange causing the axle to shimmy back and forth while contacting the brakes. Your also probably getting a little noise from the axle tapping the pinion shaft of the spider gears.
When you apply the brakes your absorbing the free movement of the axle floating in and out muffling the noise.
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