Will an auto tranny out of a 89 3.0 4runner bolt up to a 94 3.0 4runner with an auto without any or some modifications?

 

I don't know why it wouldn't. You're going to have a speedometer cable vs. speedometer wire dilema though. I'm pretty sure of that anyway. If that's the case you can swap the old parts to the newer transfer case. So you'll able to use the cable with it. Or are you just talking about the transmission and not both?

 

Yep it should bolt right in. Just need to swap the electric speedometer for the cable, like MudHippy said.
Pretty sure all the other plugs should be the same.