Been here and done it all. CrippledPetey almost had to drag me through the Rubicon the first time this issue started to come up. So... Here is the wonderful news, it could be fairly inexpensive and easy to fix, (with patience and the right extensions) or a royal PITA.
IF, 90+% of the time your 4.0 runs just fine (if not perfect), then one or both of these is almost assuredly the issue.
Starting with the "easier" route. Replace the Crankshaft Position Sensor (CPS). There are a ton of write-ups and a few videos on this. Just be careful as they mention to not drop one of the two bolts into the hole in the transmission bell housing. I did this replacement in about 20-30 mins being patient and only swearing about 10 minutes at my lack of wrist contortionist skills.
Drive and see if your issue is resolved. (Veteran wheelers running 4.0's have told me to keep a spare CPS for the trail, and I have listened).
If your issue presents itself again? Now you know it IS your fuel pump. Now I am not an electrician and know there are ways to test the fuel pump AFTER replacing the CPS. However I found that in regards to fuel pressure, it's spot on until the issue arises. No pre-cursor, you just sputter and stop.
The fuel pump in the XJ cherokee post 97 is only accessible by removing the fuel tank (why this is a PITA). I am a YouTube trained "mechanic", and was able to do so with only moderate fear about fumes and fire ;-)
I recommend the Bosch 67658 (Bosch 67658 Original Equipment Replacement Electric Fuel Pump
https://www.amazon.com/dp/B001C6023G/ref=cm_sw_r_awd_SejUub04TW1PQ) Amazon price of $192 is awesome and you may just want to buy it now.
Why this pump? Because this replacement is such a PITA, why not get the only full pump assembly that has everything AND near 5 star reviews. If you go any other brand? Well... Just saying I never want to do that job again.
Hope this helps and hit me up if you got questions