It typically depends on what you're doing. I focus entirely on inlines so I know the 258 and 4.0L engines will bolt up to the A-998, A-727, AW4, T-4, T-5, AX-5, AX-15 and so on but there is often issue with the communication between the engine speeds and transmission shifting behaviors when making an uncommon pairing. This is because of a discrepancy between the ignition system and the way the transmission receives information to perform each shift. When you have a carbureted engine like the 258 you will want to have a hydraulic or otherwise non-electronically controlled transmission. The inverse is true when operating from an electronically fuel injected engine but this focus is entirely centered around the automatic gearboxes.
It is the minimal electronics involved for carbureted and fuel injected engines that continues to grant us the option of installing a manual gearbox to either engine. Keeping the same bell housing dimensions across each engine is what allows the bolt up to happen without buying expensive adapters or spending excessive time checking everything for compatibility. The way I see it, the late CJ to late YJ era is as close as it gets to plug and play and because my current project depends on a rare and very bare minimum of electronics the bolt up process for each transmission is cake.