Accessing the red skull area requires you to press a switch temporarily lowering walls blocking it off, lowering paths that you have previously crossed. However, this will also lower a section of floor around the security armor on the upper level. Lower the paths, and then run toward the pedestal the security armor is on as the paths rise. If done correctly, you will be carried up to the pedestal, and the armor can be obtained. (sector 427)
When you walk off or on the gray flooring in the room southwest of the yellow skull switch, a lift will lower to the northwest of it. Drop into the hole to find a chainsaw and a teleporter; use it to be transported to a soul sphere. (sector 378)
After the blue skull door, do not jump down to the yellow skull. Instead, look to the northeast, and you may notice an opening in the northern wall on the higher level. The northeast walls of the room you're in are fake; walk through them to find a stairway to the upper level, where you can find a switch. Press it, and go back through the blue skull door to find a teleporter in the east. Enter it before it is closed off to be warped to combat armor. (sector 379)
Because of a teleporter being too high to reach, you can only get 80% Secrets outside of ZDoom-based ports.
It is possible to skip the bars opened by the yellow key (sector 216) with a strafejump (see Routes and tricks), and gain access to the switch raising the exit bridge (linedef 1687) before you are intended to. However, if you then lower the water level of the blood (linedef 2964) to open access to the red key that will open the exit, the exit bridge will drop with it. Because linedef 1687 is one-time-use only, this will render the level unwinnable.