Im currently in the process of purchasing an 06 6mt with a blown engine as a donor car to manual swap my 04 auto. Since I could barely find anything regarding the differences between both auto and manual J32a3 engines I was wondering if specifically the engine from the auto 04 would be a direct bolt on to the 06 6mt with some parts swapping, maybe some sensors are different, pipes, or even different crank components.
The only difference im aware of at the moment is the coolant crossover tube because the autos have a cooler that runs to the trans, Im positive it would be easier to buy an engine from a 6mt TL and mate it up to the manual trans and slap it into the car, but the engine i have from the auto TL is still good and would rather use it since it would just be sitting in storage if i didnt.

 

I'm not sure about all of the differences, but I know the starter is definitely different between the MT and auto.