Looking at the components in the Jim's kit, that bushing at the top next to the spring is the one that goes in the case for the shifter shaft to ride in. I have the Harley part number stashed away somewhere if I can find it.. There are 2 different ones, one longer than the other. I used the Jim's tool to remove and install the new bushing. Makes it easy to get it right. No measuring, just let the tool do it.
Did you have a look at their instructions? It says their kit is for all BT Shovel and EVO 5 speeds from 80-99. By that, you should be good to go. With the kit, or with the Harley stuff if you can find it as a pile of parts.
I'm looking at my parts book and comparing it to Ronnie's page for a 92FXRS, most of my shift mechanism internals were the same as yours. The support blocks and needle bearings were the same. Shift forks and shafts were the same. Even the shifter shaft lever with pawl and ratchet stuff was the same. The shift drums were the only major difference.
I did this about 8 years ago, one of the better mods I've done to my bike. Here is a link to when it was going on, sorry not much detail. In addition to the shift drum and the pawl assembly, you would need the pillow blocks, as they do away with the plunger detent in favor of the roller detent. I think my total cost was about $125, not bad.
Are all the upgraded internals a direct replacement into the transmission of my 2000 Lowrider. It shifts OK between gears, but neutral is hit or miss. More miss when it gets good and hot. What was the first year that incorporated all the improvements? It looks like 2003 for sure, maybe 2002...
www.v-twinforum.com
If you could find a take off shift mechanism from somebody that upgraded to 6 speed internals, that would be best. Looks like you could go all the way from 01 up to 05/06 for a donor bike. I got mine from online auction. Everything was stock Harley parts and fit just like they were always in there. I reused my shift forks and shafts, they were in good shape. I did buy the bushing from the dealership. I also needed the new centering screw. You might need to do some further research for the neutral switch for your FXR. They go from always in contact with the drum to only in contact when in neutral, less friction for shifting. The only problem with my install is I get a neutral light in 5th too. Probably has something to do with a difference in top covers.