If your pinion seal is leaking, you should replace it. 0.003-0.006 is the normal allowable pinion to ring gear backlash measured inside the differential with a dial indicator. When testing pinion backlash from the outside with the driveshaft, keep in mind you are also feeling all the slop in the spider side gears and axle gears and it adds up. Only true way is to open up differential and inspect everything closely.
Clunk you hear is most likely the weak factory upper rear control arm bushings, at the body mounting location up right under the rear seat, are worn out and allowing a lot of movement of the control arm when going from F to R. It will actually allow the metal control arm to make contact with the metal body making a loud clunking noise even when the transmission upshifts or downshifts or goes from F to R.
Best solution is to replace the crappy weak OEM control arm with a IronRock control arm. Bushings are much stiffer and are replaceable if they ever get weak which they will not. The IronRock control arm also has an adjustable HEIM joint on the differential end mount that is greaseable and rebuildable. This allows for adjusting and setting pinion angle correctly when installing a lift kit.
This arm was designed for the much larger and heavier Jeep Grand Cherokee (WJ) so it is super heavy duty for the smaller Jeep Liberty.
Control Arms - Iron Rock Off Road
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Supporting Vendor and Moderator of LOST05 Jeep Liberty CRD Limited
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