On your way through the storage room to the switch enabling access to the red key, one stack of two crates has a tiny, inexplicable gap between them. Press on the bottom crate, and it will turn out to be a lift, leading you to a soul sphere and a box of rockets. (sector 31)
Once you enter the building where the red key is, a section of the central building's east wall will lower, revealing two arachnotrons. In this room, you will find an alcove with a box of rockets at the north. Press on the tile at the east side of the northern wall to find combat armor. (sector 205)
In the room immediately following the red key-locked door, flags hang at each corner. Push on the southwest flag to find a soul sphere. (sector 243)
Due to the way in which the level's REJECT lump is composed, all monsters in sector 293 will be unable to detect your presence, even if you are standing right in front of them, and will not move until they are attacked. Furthermore, all actors standing in this sector are immune to blast damage. Whether this was intentional or not is unknown.
The lift involved in secret #1 consists of two sectors: an outer sector (sector 30) and an inner sector (sector 31.) However, both the front and back sides of the lines separating the two sectors (linedefs 226, 227, and 228) are untextured, and it is possible to block the outer sector while the inner sector continues to rise. If this happens, a hall of mirrors effect will be visible until the outer sector rises.