I know a whole bunch of folks who like 5speeds for wheeling... different strokes for different folks.
I actually just checked my parts catalog... if you had a 2.1L diesel, you'd need a new bell housing. Apparently the 2.5L diesel uses the same bellhousing as the 4.0 though! Both use the 5300 8158 bellhousing.
I'm not sure but you may need to use a different clutch and flywheel etc however. I'll update this post shortly after I've cross-referenced those numbers.
EDIT: you'll need a different rock/dust shield as noted above, you want a 5300 4473.
You will need a different drive plate (5208 7578) a different cover/spring plate (4713 323) and some nuts and bolts. Just get a clutch replacement kit for a 4.0/ax15 and I think you'll be good to go.
You will also need a flywheel/ring gear for a manual as noted above, the number I'm seeing for that will be a 5300 5524 (flywheel and ring gear as a kit) but you can get those from any aftermarket vendor you want as well.
You may need to get the ECU from a manual 4.0L, but on a 95 I think you can probably just disconnect the wiring from the TCU to the trans and let the TCU sit there doing nothing. 97 and later you'd run into issues with a CEL and codes thrown.