Hi, CJMall...I have some very interesting news regarding the nut in your illustration. After close research through all Mopar service references from 1989-99, it's clear that this is not a Jeep counter/cluster gear. All Jeep applications of the AX15 use a selective fit snap ring behind the 5th gear, not a nut.
All Jeep/Mopar parts references to the AX15 transmission also show the use of a selective fit snap ring at this location, not a nut. The unit in my step-by-step, two part series on the AX-15 is early '90s, and I have a 1998 Jeep TJ Wrangler Mopar shop manual that also shows the snap ring use. I checked my Mopar TechAuthority subscriber info to see if 1999 uses a nut instead of a snap ring. Not so for Jeep AX15 transmissions.
Here are two PDFs showing 1989 and 1999 parts layouts plus the entire 1999 Mopar parts listing for both the later AX5 and AX15 transmissions for those seeking genuine Mopar parts access for the later TJ Wrangler or XJ Cherokee:
1989 AX15 Countergear and 5th Snap Ring.pdf 65.09KB
5th Gear Snap Ring on AX15.pdf 97.44KB
AX15 1999 Jeep Transmission Parts.pdf 701.48KB
As for the nut being there in the first place, I looked further to provide an explanation. Your AX15 transmission is a "rebuilt" unit, and therefore subject to available parts from cores. Toyota uses the AX15 as the "150" transmission, and I went into my Toyota OEM shop manuals. In the 1993 Toyota T100 shop manual, I found the countershaft/cluster 5th gear end with a nut instead of a snap ring. You apparently have a Toyota transmission countershaft/cluster gear with the 5th gear hold nut.
Toyota wants you to use a "hammer and chisel" to open up the staking in the nut. (If there are two stakes, the nut has been reused. The current stake in the shaft slot is the one you need to open.) I suggest making a narrow, wedge shaped pry tool from an old chisel. Shape the end to just fit into the shaft slot. With care, you can tap inward with a hammer, which will pry out the indented nut flange without damaging the machined slot.
The Toyota torque figure for the re-torque after installation is 94 ft-lb or 127 N-m. Make sure you stake the nut flange into the slot after torqueing the nut. If the stake area of the flange is fresh, the nut often gets re-used. If you want to replace the nut, see your Toyota dealer and not the local Jeep dealership!
Will all of this work together? If the gears and synchronizer assemblies are a matched set and all tolerances match with Jeep or Toyota figures, this can work. There are apparently interchange possibilities here, as your counter/cluster gear indicates. However, if tolerances, spacing, gear mesh, synchronizer parts alignment, gear alignment or other problems exist with this parts "mixing", you may have unearthed your shifting problem. Problems can occur even when mixing strictly used Jeep parts, so rely on actual measurements and the true fit/alignment of parts. Again, see my two-part article for details...
Let us know how the Jeep-Toyota marriage works out. Check out the parts alignment between gears and positions on the shafts, gear backlash, synchronizer parts fit and for any signs of mismatched or misaligned pieces.