Are we sure the gear ratios on the AX15/NV3550 would be appropriate for the diesel? Not sure how the powerband/rpm range of the 4.0L compares to the 2.8, but it may be "close enough for government work".
I'm pretty sure a guy I know through work (in a field office in Colorado Springs) has/had a 5-spd diesel KJ, so fairly sure they offered manuals here, in which case I'd just go with the stock clutch parts.
If you do get a factory manual trans, make double-sure to get the transfer case and both driveshafts from the donor too - there's a small chance the input shaft spline count on the t-case could be different between manual and auto, and very likely the transmission itself is a different length (this is a known thing in the older XJ line, where swapping the AW-4 automatic for either the AX15 or the NV3550 shifted the position of the t-case slightly due to overall driveline length, requiring the manual donor's driveshafts.