Nice YJ ! You can expect to need a complete set of metric and SAE tools on hand and there's no rhyme or reason as to which one to use.
Mostly depends on what part you’re working on. Like on the 4.0 starter, you have one bolt that’s standard and one is metric. People would assume that’s just a random thing that happened, but really it’s because one bolt threads into the starter and one threads into the bellhousing. Starter was made by Denso for Mitsubishi who supplied them to Jeep. Asian part, so the bolt thread was metric. The other hole is threaded at the bellhousing which was an American made part, so the hole there is SAE.
Engine block, all standard except for the random knock sensor hole that they added for the 1987+ Renix which used a sensor that was a metric thread. They left that hole there on the 01+ XJ and YJs that didn’t have knock sensors (because they had Chrysler fuel injection that didn’t need it) so as far as I know, that’s the only SAE engine bolt.
Tub is pretty much all SAE except maybe the torx bolts for the dash? I don’t recall their thread. Hinges, seats to floor, etc are SAE.
Intake manifold I believe is all metric.
Axles are all standard themselves. The front axle unit bearings however are metric because those bearings are a foreign part by Timken, so they are that odd 12mm coarse thread with the 12-point 13mm head. Brake bolts and such are all SAE.
The manual transmissions and tcases are weird. I’m pretty sure the bellhousing bolts (to transmission) are standard but I’m not sure I used a 9/16 on them but maybe 14 would have been correct. Not sure of thread. Fill and drain plug (transmission) are 24mm hex, not sure of the thread. The shift tower bolts I believe are metric but because the tcase shifter hangs off two of them, they have a standard thread on top of the welded nut and use standard nuts to secure the tcase shifter. The tcase shifter bolts to the side of the transmission also with a metric bolt since it’s the transmission. Bellhousing to engine bolts are all SAE because engine block. Same for flywheel and clutch. Tcase is an oddball, there is a random 10mm 12 point long bolt, I’m pretty sure the others are all metric but it’s been a while. As far as I know the studs and nuts that hold the tcase to the transmission are SAE and 9/16, but maybe the thread is metric and it would have worked with a 14mm also if I tried.
Long story short, yeah ya need all the tools lol. Maybe that helps clear it up a teensy bit though (or maybe made it more confusing). After many years of working on them you kinda start to just remember what is what. Of course, all that means is you’ve spent a shitload of time working on the Jeep over the years. Hopefully that’s a good thing.
I’m glad that nowadays, pretty much everything is 100% metric. I’m fine with understanding either of them in my head (fractions vs 10s and mm’s) but it’s really nice to only reference one set of tools.