cant believe nobody wrote on here the secret locations, guess ill have to do it.
1.in the room with two wheels, have both of them point down,exit, down,continue, bottom left,left,left, down(you may notice that this room is upside down version of what it was).
2.in the egyption room, turn the wheel so that the room on the right is old, then go all the way back out to the ledge(make sure to change the position in the two wheel room, otherwise you cant get out), take a left, and then yes, its now possible to make another left to the secret place. learn who thoth is.
3. on the screen in the room where you get the cube, place 1's all around the center zero, then take the elevater down, go left past the one you came up from into the next pipe to the secret room.
4. with the newly aquired connection pod, head towards the ledge exit (without secret room one getting in the way) and head back till you find an old rusted version on the relocater that you use at the end of the game, put the pod in and enter, you dont go anywhere but its a secrete place.
5. deactivate protocol 54-4, go back to the first pod entry(other than secret room 4) and you'll see a new path down which is the last secret room.
hope my directions were clear enough.