From the area near the start where all the shotgun guys are, turn left (south) and open the wall behind the light for a super shotgun (#1).
Continuing from the area described in secret #1, head west and down a small flight of stairs until you reach a door. The wall to your right has a white grate on it. Pull it down and it will lead to a soul sphere (#2).
Just to the left of the blue keycard is a very narrow switch. Lower it, then head back one room. Opposite the white grate, a passageway has opened. Follow it (#3) to collect all the chaingunners' ammo, as well as a chainsaw and berserk pack.