My 1995 Toyota 4runner recently got attacked by a large puddle/small lake. Sucked water and busted a rod. Now I am looking at replacing the engine (V6 3vz-e) with one I got from a friends roll over 1995 4runner.

So here is my question:

My toyota is an automatic. The engine I have to replace my busted one was pulled from a 1995 manual transmission 4runner.
Will the engine from the manual 4runner work in my automatic? Are there any parts that need to be switched or changes? I am very new to yota mechanics and would love any help you all can offer!