In secret #2, the sector where the chainsaw, the southern three health and four armor bonuses are on, counts as a different secret (sector 633). Entering it opens the southern wall, releasing two demons.
From secret #3, move southwards. The opened wall itself counts as a secret (sector 631).
From secret #4, move southwards. The room where the two demons came from counts as a different secret (sector 632).
From secret #2-5, go back to the blue door. Run towards the previous secret, a tripwire will activate a door in the recessed northern wall of the alcove, allowing you to jump to a platform holding a green armor (sector 157).
After using the skull switch atop of the central tower, look to the southwest where you see a door. Run towards it, thus climbing the wall in front of you and jumping over the next wall, landing on the stairs that started raising by pushing the switch. (Of course you can also walk back to the tower's base and climb the stairs.) Ascend the stairs and enter the door atop. Proceed to the "hub room" where are three skull switches. Open the (switchless) western wall to find a passage (sector 311), waking up a cacodemon. Pick up nine armor bonuses and a computer map.
Push the southern skull switch in the hub room to reveal a door that you enter. Follow the path to your left until you reach a wooden door with skulls on it. Behind the door, drop down to the east into the lava and ascend the stairs behind the corner to your left. There is a ledge (sector 226) upstairs where you find three health bonuses and a super shotgun. Drop down to the north and follow the bend to the west to return to the blue door east of the central tower.
Face the yellow door in the south of the hub room and descend the stairs to your left. Pick up the radiation suit to the north and return to the lowermost stair. Face southeast and sprint over the lava along the wall to your right, following its bends. It leads to a stone floor with a string of armor bonuses on it. To the southwest is a tower, push the switch at its southwestern side and enter the teleporter to get to the cage (sector 227) holding the yellow skull key, a medikit in front of a skull switch (that you need to use in order to access secret #10) and a teleporter.
After using the teleporter in secret #9, ascend the stairs and return through the hub room to the central tower. Climb it until you see a platform with a yellow door to the north, unreachable since there is a wall preventing you from jumping on it. Continue ascending the stairs to the tower's southeast. Look to the north again and note the triangular part of the floor (with a medikit on it), cutting in the tower's wall. Open the wall to the triangle's north, revealing a switch. Using it lowers the wall in front of the yellow door's platform, where you find a berserk pack. Enter the yellow door to get ambushed by three troopers, three imps, a pain elemental, a cacodemon and two demons. Downstairs you find a bulk cell, six health bonuses and six armor bonuses. Open the western wall for another cacodemon, two more demons (you probably killed before through the window) and a passage (sector 371) to the BFG9000.
Use the skull switch mentioned in secret #9 to lower the pillar (sector 238) where the soul sphere rests on.
Enter the yellow door in the southeast of the hub room. In the northwestern tower you find a shell box, a box of rockets and two bulk cells. Enter the walkway with the five armor bonuses to open the southeastern tower's center, revealing an ambush, another super shotgun and three bullet boxes. Use the skull switch there to open the northwestern tower's center and the pentagram stone wall behind the bars to the north, both revealing ambushes. After killing the monsters, enter the now opened room north of the bars to find a bullet box, six health bonuses and a blue armor.