While a lot of things are possible, for the Pinion bearing to make a
CLUNK, it would have to be very loose. So loose that visible in/out play would be evident.
Grab the pinion and try to move it in and out. If it moves at all, there is no pinion bearing preload. This is bad.
U-joints tend to make a more distinctive click/clunk. The noise pinion bearings make is less distinctive. It is higher pitched because it varies with engine speed.
Bad Carrier bearings are lower pitched noise because it varies with the speed of the tires.
How many miles on the car? When was the last time the rear-end was serviced? If more than 100k miles, recommend a service. Almost all rear-end problems will become evident upon visual inspection of the gears and oil.
However, when abused, U-joints fail at a much higher rate than the rear end. IMO, the first inspection should be U-joints. Then move onto the rear-end.
From the Ford Service CD:
Universal Joint (U-Joint) Wear
Place the vehicle on a frame hoist and rotate the driveshaft by hand. Check for rough operation or seized U-joints. Install a new U-joint if it shows signs of seizure, excessive wear, or incorrect seating. Refer to Section 205-01 .
Axle Noise
NOTE: Before disassembling the axle to diagnose and correct gear noise, eliminate the tires, exhaust, trim items, roof racks, axle shafts and wheel bearings as possible causes. Follow the diagnostic procedures in Section 100-04 .
The noises described as follows usually have specific causes that can be diagnosed by observation as the unit is disassembled. The initial clues are the type of noise heard during the road test.
Gear Howl and Whine
Howling or whining of the ring gear and pinion is due to an incorrect gear pattern, gear damage or incorrect bearing preload.
Bearing whine is a high-pitched sound similar to a whistle. It is usually caused by worn/damaged pinion bearings, which are operating at driveshaft speed. Bearing noise occurs at all driving speeds. This distinguishes it from gear whine which usually comes and goes as speed changes.
As noted, pinion bearings make a high-pitched, whistling noise, usually at all speeds. If however there is only one pinion bearing that is worn/damaged, the noise may vary in different driving phases. If pinion bearings are scored or damaged or there is a specific pinion bearing noise, new pinion bearings must be installed. A worn/damaged bearing will normally be obvious at disassembly. Examine the large end of the rollers for wear. If the pinion bearings original blend radius has worn to a sharp edge, a new pinion bearing must be installed.
NOTE: A low-pitched rumble normally associated with a worn/damaged wheel bearing can also be caused by tires.
A wheel bearing noise can be mistaken for a pinion bearing noise. Check the wheel bearing for a spalled cup, and spalled/damaged rollers. Check the wheel bearing for rotating smoothness and end play. Install a new wheel bearing if any of these concerns are detected.
If the wheel bearing is damaged, the roller surface on the axle shaft may also be damaged. Install a new axle shaft if any damage is detected.
Chuckle that occurs on the coast driving phase is usually caused by excessive clearance between the differential gear hub and the differential case bore.
Damage to a gear tooth on the coast side can cause a noise identical to a chuckle. A very small tooth nick or ridge on the edge of a tooth can cause the noise.
Clean the gear tooth nick or ridge with a small grinding wheel. If the damaged area is larger than 3.2 mm (1/8 inch), install a new gearset.
To check the ring gear and pinion, remove as much lubricant as possible from the gears with clean solvent. Wipe the gears dry or blow them dry with compressed air. Look for scored or damaged teeth. Also look for cracks or other damage.
If either gear is scored or damaged badly, install a new ring gear and pinion.
If metal has broken loose, the axle housing must be cleaned to remove particles that will cause damage. At this time, any other new parts in the axle housing must also be installed, if necessary.
Knock, which can occur on all driving phases, has several causes including damaged teeth or gearset.
In most cases, one of the following conditions will occur:
A gear tooth damaged on the drive side is a common cause of the knock. This can usually be corrected by grinding the damaged area.
NOTE: Measure the end play with a Dial Indicator with Bracketry and not by feel.
Knock is also caused by excessive end play in the axle shafts. Up to 0.762 mm (0.030 inch) is allowed in semi-float axles. The frequency of the knock will be less because the axle shaft speed is slower than the driveshaft.
Clunk is a metallic noise heard when the automatic transmission is engaged in REVERSE or DRIVE. The noise may also occur when throttle is applied or released. It is caused by backlash somewhere in the driveline or loose suspension components; it is felt or heard in the axle. Refer to Total Backlash Check in this section.
Additionally, clunk may be heard upon initial drive-away. This occurs as engine torque shifts vehicle weight, forcing changes in driveline angles, preventing the driveshaft slip-yoke from sliding on the output shaft. To correct for this condition, lubricate the slip-yoke splines.