It is still possible to change and manipulate the sprites and floors, its just more difficult to do, and very difficult to figure out a scheme for potential distribution of changes. The DOOM.WAD file must be changed, and that is a pain. All the sprites follow a naming scheme. The first four letters are the sprite's name, or and abbreviation. TROO is for imps, BKEY is for the blue key, etc.
Monsters are the most complicated.
They have several different sequences, for walking, firing, dying, etc, and they have different sprites for different angles. Each picture has three sections, basically. First, a four-integer header. Then a number of long-integer pointers. Then the picture pixel color data.