I know it is too late for you as ya have the tranny out but when we had this sort of problem often we would set the vehicle up on a lift and run it while poking around underneath to pinpoint the problem. This can be dangerous if you don't have the vehicle supported well, so be really careful if you try it. � The best way to do it would be a drive on platform lift , using jacks to lift the rear axle (or both if it only shows in 4WD) If you have a friendly shop nearby that doesn't mind ole jeeps, it may be worth paying them to do this... �A stethescope and a pry bar help to locate mystery noises. (Harbor Fright has the Stethescope.)
Some possible rattle points....exhaust system, pedals,clutch and brake linkages, shifters, sheet metal panels, loose parts in the toolbox or on the floor, driveshafts (out of phase, bad u joints, loose yokes) parking brake assembly and linkages, throttle linkage, �etc, etc.
On your clutch look for loose springs in the driven disc, or a loose center assembly. The pressure plate could also have loose parts.. Striking the flywheel lightyly with a deadblow hammer may reveal a rattle which you can then track down, if it is in the clutch.