When you enter the north of the building, look behind the spectres at the east, and you will notice a skull switch on the wall. Shoot it, and a door will open to the west, leading to a backpack. (sector 99) Note that if you raise the stairway and reach the switch at the apex, the other switch will be closed off, and this secret will become inaccessible if you have not opened it already.
At the east of the building, in the corridor where the switch to access the blue skull is found, the sides of the corridor have metal plates bearing a pentagram, a devil face, and an upside-down cross. The northwest portion of the wall, however, does not. Open it to find a secret passageway, and then open the wall at the end to access the chaingunners' cage from earlier, as well as security armor. (sector 55)
Because a berserk pack is locked away in the inaccessible Deathmatch portion of the level, it is impossible to get 100% items on this map.