I don't think ball-joints would would clunk like this in an XJ. They are easy to check just by jacking up your Jeep just high enough so that the tires clear the ground. Grab your tires at the top and bottom (without putting you fingers under the tire) and see if you can move the tire-wheel in a push pull movement. If you have play there your ball joints or unit hub are bad.
It seems to me this is really a control arm issue either axle or body side bushings. They don't need a lot of play in them to make a clunk that is heard and felt from the floorboard.
As Crispynuggets has pointed out bad u-joints on either the front or rear drive shafts could cause a clunk like this that may be transmitted to the floorboard.
95 Cherokee SE 4.0, 5-Spd, 8.25;
6.5" Rusty's Lift, Atlas II Rims, 35x12.5x15 Wild Country,Rusty's Tube Bumper, Wilderness Rack
Rock Sliders, K&N Panel Air filter, PSC steering box,
I-ROK reinforcement kit, ORO U-TURN steering kit,Conversion Headlights/Silverstars And too much $$$