Well after looking at several different options, I decided to go with a slightly less powerful alternator, but one that would be a direct bolt in, no extra wiring needed. I believe this is actually a popular swap, but I have yet to see any writeups, or detailed information, so here you go:
Factory my YJ came with a 90 amp alternator, part number 13199.
13199 can be found on:
97-98 Dakota 2.5
91-98 XJ 2.5, 4.0
91-92 MJ 2.5, 4.0
92-98 ZJ 4.0
91-98 YJ/TJ 2.5, 4.0
The replacement was 13387, the look up I used was a 98 3500 Ram 4WD V10. Its rated at 136 amps, the one I got peaked at 172 amps output.
13387 is an option for:
97-99 Dodge B-Series Vans 3.9, 5.2, 5.9
97-98 Dodge D,W-Series Trucks 3.9, 5.2, 5.9, 8.0
97-99 Dakota 3.9, 5.2
98-99 Dakota 5.9
97-98 ZJ 5.2, 5.9
13387 comes with a 7 groove pulley, so I used my 6 groove pulley on my old alternator. The 7 groove pulley will work, so you could leave it. However, there is an advantage to using your stock 6-groove, its 20% smaller. 20% smaller makes is spin faster, thus the alternator creates more power, sooner.
My factory alternator, I've already switched the pulleys here, so its got the 7 groove off of the other one:
New, the casing does get 0.5" larger, but the mount points are the same:
This was the output of the alternator I got, and remember that graph and figure will be moved if you use the smaller pulley, like I did, so this chart is with the larger pulley obvisuly:
New one all bolted in:
It is recommended that you upgrade the charge wire for the alternator to at least a 4 gauge wire.
The alternator set me back $125, but it does have a lifetime warranty.
If you need more power, I found 145-160 amps solutions that would bolt up, from Dodge-GM, but there would be some wiring involved.