I just put a 94 runner body on my 92 standard cab frame. Runner was a v6 auto. My truck was a 22re 5spd. The wiring harness was plug and play. So if you wanted to keep fuel injection it's easy. Just find a 22re close to the same year as yours. But like they said trans and motor mounts would need...
If the ac compressor is still working when warmed up, check your heater core water shut off valve. Sounds like it's not stopping the flow of water. So once the engine is up to temp the heater core is too, heating the air after it leaves the evaporator. The fan is always blowing air through both...