Something that Puzzles me
I took a quick look, but I can't work out where the gamefiles are read (namely GAMEMAPS and MAPHEAD). Can anyone help?

Uh...try the tutorial at Die Hard Wolfers on changing the file names, it should show you there.

Yeah, but thats names. Its not quite wat I want, but thanks man.

Most of the stuff you're looking for can be found inside ID_CA.C. The bulk of the map level loading takes place in CAL_SetupMapFile. Later, the mapsegs info (besides a few things like floorcodes) get copied into near data arrays and structs inside SetupGameLevel of WL_GAME.C. Just incase you still wanted to know. ;)