All manual XJ,YJ and TJ 4.0L had the AX15 from 1991/2 onwards till 1999/2000 when the NV3500 came along. This itself was superceded by the 6 speed mercedes transmission in 2005. The 2.5TD XJ also had the AX15 and NV3500. 2.5L petrols had the lighter duty AX5 or NV1500 which aren't any good in a 4.0.
The AX 15 is a tough and reliable unit. If you only have a problem with 3rd gear, it might be worth having it repaired, as buying used is always a risky business even if you get one with a gaurantee from a dismantler, as you're still going to have to go through the hassle of fitting it and removing it again if it proves fauty. As IOM says, you could also fit the NV3500 from a later mode if you can find one, it's not a straight swap, there a re a few other bits to change with it but it is a stronger transmission, but as stated the AX15 is pretty tough anyway.
Converting to auto is also possible, but much more work.