How's the boomerang bushings and rear upper ball joint? Those weak rubber bushings at the body end of the boomerang tend to get real weak fast and allow a thumping noise especially when the transmission upshifts or downshifts. This thumping noise can be heard real loud inside the cabin since the upper control arm (boomerang) bolts directly to the underside of the cabin, not the frame, right under the rear seat area.
The super heavy duty IronRock rear upper & lower control arms are the best you can buy to upgrade the rear suspension and make it bullet proof.
As to the springs, upgrading to the IronMan 4X4 America springs, front and rear, or the OME springs is your best choices.
Neither is cheap, but if you want quality, you have to pay for it.
https://www.ironman4x4.com/collections/coil-springsThe rear springs being a little loose when you have the vehicle on a lift with the rear axle at full droop is normal.
If you want a good ride and good handling, get the Bilstein shocks/struts front and rear, they are some of the best there is on the market.
Struts/Shocks:
Bilstein Brand: 4600 Heavy Duty (B6)
Part Number Position
24-139168 Front
24-139175 Rear
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Supporting Vendor and Moderator of LOST05 Jeep Liberty CRD Limited 
Ironman Springs/Bilstein/Shocks
Yeti StgIV Hot Tune
Week's BatteryTray
No FCV/EGR
Samcos/ProVent
SunCoast/Transgo
Carter Intank-pmp
2mic.Sec.Fuel Filter
Flowmaster/NO CAT
V6Airbox/noVH
GM11 Bld.fan/HDClutch
IronrockArms/wwdieselMount98 Dodge Cummins 24 Valve