The Series III motors include many changes. The upper intake manifold is now aluminum on the naturally aspirated models. Intake ports are mildy improved, 1.83" intake valves (instead of 1.80" as on Series II) and 1.52" exhaust valves were introduced in 2003 engines, just before switching to Series III. Electronic throttle control is added to all versions, as is returnless fuel injection. Stronger powdered metal sinter forged connecting rods are used in 2004+ supercharged, and 2005+ naturally aspirated engines, instead of the cast iron style from Series II engines. Emissions are also reduced. In 2005, it was the first gasoline engine in the industry to attain SULEV (Super Ultra Low Emissions Vehicle).
Also note that Series III engines are the base for any 3800 produced for the 2004 year and up. This means the same block, heads, & connecting rods apply to any remaining Series II engines made after 2004 also. The difference is that Series III engines received the new superchargers (Generation 5 - Eaton m90 - if equipped), intake manifolds, fuel systems, and electronics.