In Theory... An exhaust manifold made by say ATS should fit an industral 12v engine?

As in bolt right up

 

in theory...yes

 

yes it should i work on machines and they look the same but depends if it none turbo or if it is turbo it may be different cuz of how the turbo sits

 

Don't some industrial/med duty trucks have the turbos low and to the rear, like the 3rd gens?

 

turbo position under the cab is not a problem, I just need to know if a 12v Ram CTD mainfold will bold on to a 12v industrial engine and i can plumb my own turbo setup..

This engine also needs an intercooler

 

I can't see a reason it won't, the head castings are pretty much the same.
The primary differences between industrial and automotive engines are the pistons (automotive pistons are usually hard anodized on top) and the injection systems and line routing. The injection pump can be anything from a CAV, to a Bosch VE, P-pump, or a Nippendenso inline pump.