The engine doesn't care if it is driving a torque converter or a flywheel. There are two things that could be different between an automatic an manual transmission. For the manual transmission there needs to be a small pilot bearing in the end of the crank shaft. That keeps the clutch disc and the transmission's input shaft centered. If you need that bushing but it's not there, it takes about a minute to pound one in. If the end of the crank shaft is not drilled for that bushing already, (most are), it will need to be drilled by an engine machine shop.
In some cases the profile of the camshaft will be different. That sets the "personality" of the engine. With an automatic, you basically hold steady pressure on the accelerator pedal. With a manual transmission, you are on and off the gas often and they may have made subtle changes to the shape of the camshaft lobes. It is unlikely you would even notice that. I suspect that pertains more to much older cars that used carburetors. They could only be most efficient at two speeds; idle and highway speed. With electronic fuel injection, the fuel system can be fine tuned for any set of conditions.