In the outdoor nukage pool, the vantage point the Revenants attack you from can be climbed onto from the northwest side. Here, you can find a box of rockets (two on Hurt Me Plenty or lower,) a rocket launcher, and a switch. (sector 56) There is a radiation suit in the north-western mine, and you can leave the nukage pool by lowering the walkway in the south.
After pressing the switch in secret #1, inside the northeast mines, you can find a switch in the northern alcove just after the Chaingunner ambush. Press it to open an alcove in the southeast, containing a Hell Knight and three medikits. (sector 176)
After pressing the switch to access secret #2, once you get the yellow key and return to the entrance into the mines, there will be a new switch at the alcove directly north of it. Press it, and return to the room with the pillars near the start of the map to find that a new alcove has been opened to the west, containing a backpack and a plasma rifle. (sector 185)
Within the checkerboarded hall leading to the exit teleporter, there is a section of the west wall that violates the pattern in place throughout the hall. After obtaining the blue key, press on this section to open it. Here, you will find a river with health bonuses strewn across it, broken in the middle by a waterfall with a Chaingunner, two Sergeants, and two armor bonuses at the opposite end. Directly northwest of the waterfall is a soul sphere. Jump from the waterfall to the soul sphere to trigger this secret. (sector 287) Secret #3 can be accessed from this location as well, by opening the door at the end of the tunnel, which leads to the start of the map.
In the cage opposite of the one containing the switch to lower the blue key, there is a portion of the west wall where the ridges are not as thick as the rest. Push on it, and it will lower to reveal a switch. Press the switch. When you reach the portal, the pillar with the megasphere on top of it will have lowered, allowing you to take it. (sector 339)