1) All scripts in the Dungeon Generation folder and the Assist Scripts folder, plus the obj_dungeongenerator object. That should be enough, if you change dungen_render_tile to spawn whatever objects your game uses (instead of the placeholder tiles it uses now).
2) You don't need any special behavior in the player, it's completely separate from the dungeon generation system. (You can always check playerstate_normal and the obj_viewcontrol if you want to see how the camera is controlled)
3) Currently the pattern sprites (the sprites that are used for the floor/wall patterns) are assigned in dungen_rooms_assign_biomes, you can edit this script to e.g. pick different sprites depending on what floor you're on. The tilesets uses for walls, floors etc are set in obj_demosetup, you can set these variables based on current floor / area to control the parameters.
4) You should use a surface the size of the screen, and move it around based on the camera position, right???
5) Yes, dungen_rooms_assign_biomes currently always uses the same chance for every floor but you could edit it to pick different tilesets / pattern sprites depending on which floor you're on.