Once you remove the front driveshaft, everything in the front axle is still rotating, only thing not rotating is the removed driveshaft!
Have you felt of the pinion shaft with the driveshaft removed? Should be NO play, it should be good and tight. NO up and down or side to side feelable movement!
Replacing the pinion seal only involves removing the driveshaft and the pinion yoke, nothing else. Without disassembly of the whole front axle, it does involve tightening the yoke back to the required torque to achieve the correct rotational preload on the pinion bearings. If the yoke nut was overtightened or under tightened, it could cause vibration problems!
You really have to be careful when you work on pinions....
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Supporting Vendor and Moderator of LOST05 Jeep Liberty CRD Limited
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