In the building in the south of the blue skull key, there is a green armor on top of a small green platform. Walk diagonally up into the tan colored wall area with blood on it to reveal a room (sector 497) with twelve health bonuses and a blur sphere.
After falling down from the ventilation shaft on a green armor, you will enter a room with a long curved staircase and barrels. Open the back wall of the eastern alcove to reveal a blue armor in a secret shortcut (sector 426) back to the ventilation shaft.
After entering the yellow-key door in the open area with the spider mastermind, enter the teleporter which teleports you to the other door requiring the yellow-key. Return to the door you used to enter this hallway for the very first time. Turn around and go through the new opening in the eastern wall to enter a secret room (sector 133) with four backpacks. In here, open the back wall in the alcove to the east to kill two (one on easy skill levels) chaingunners and find six rockets and 4 shotgun shells. Due to a limitation of the game engine, you can open a passage and a window between this hideout and the teleporter right south of the yellow door by pressing the use key on "invisible triggers" right after going through the yellow door. So the secret room also can be entered from the chaingunner's hideout. (The "invisible triggers" in fact are part of the bars that will block the yellow door while fighting the cyberdemon. Pushing those from the yellow door side or the switch in the cyberdemon's circle not only will remove the bars, but also open the passage between teleporter and hideout.)
In the large open area with the tunnel that looks like intestines, right before entering the tunnel walk along the ledge on the west wall to enter an area with a soul sphere (sector 59).
Fall into the well at the map start to find a medikit and a box of shotgun shells. Push the switch to raise the ground so you can exit the well.