I know the heads flow better but I don want to change anything else. Can I just swap the Gen III heads and reuse my Gen II manifolds?
No, the Gen III heads have very different intake port locations and angles of port entry, they don’t line up at all. You cannot “port match” either to make them fit. The exhaust port shape on the Gen II engine is a “Round” exhaust port, the Gen III’s use a “D” shaped port where the flat edges of the “D” would hit against the opening of stock Gen II exhaust manifolds.