Main thing is camshaft, the heads fit a teeny bit better and the bore x stroke ratio is closer to the ideal due to a teeny bit bigger bore (a pube each side of the slug) plus the use of a lighter intake valve means... the 6.2 is slightly better suited to high rpm operation (HP). Valve springs, pistons and rings, are different spec as a result.
That year automatic SS featured AFM cylinder deactivation via ECU controlled collapsible lifters and from September with the Series II also revised camshaft, Ethanol Flex fuel capability, and same engine for manual and auto. This introduced greater efficiency (reduced fuel consumption) and comparable torque with huge drop in emissions.