Dwayne can be found stuck inside the helicopter you see near the beginning of the level. Shoot the glass and button inside, and it will open up for you to rescue him.
Dwayne has been moved completely, and is now found much later in the game (possibly to balance the level out). After passing through the pipes area (after you destroy the Robot Transformer and taking the elevator up to the next floor, there are two pathways. The one on the right will lead you to Dwayne, who is next to a Rico Telepoint. Use the gears to push you under, and then use them to push you up. Leap off to the metallic walkway, and rescue Dwayne.