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It really depends on how long it was driven with no transmission fluid. If it lost the fluid, presumably through the transmission line leak, there is a good chance the transmission was not damaged if you did not continue to drive it with no/very low fluid. The leak could probably be replaced, the transmission filled back up and you could be good to go. If it was driven until the transmission began to slip or no longer drive then it might have caused damage to the transmission internals.
As far as the clunk, that's pretty normal for this type of vehicle unless the fluid level is still low and it is jumping into gear. I would check the fluid level if you haven't already, the u-joints, and the slip yoke for wear and replace as necessary.
If the transmission was damaged, they aren't too terribly costly to replace or rebuild. I would guess somewhere in the $2000 range for a parts and labor.