I have to admit this game had been stumped by door 3 and after searching without success for advice I gave up. Shame because this type of game is usually my cup of tea; I just need more hints.
There is a bug which loses a picture piece. If you collect the picture piece in the cabinet with the key and then collect the picture piece on the floor in the corner of the room, your inventory only shows 1 picture piece.
I have completed the game a few times with different solutions for 000 but in 966 I always do the same thing and just open the 3 valves so that the container lids pops out. I'd never taken any notice of the position of the lines on the pipes above until I read your bug report!
I know the solution to 000 changes with each game although I have yet to see up up up. I am just about to play through again using the latest download and will see if I get a problem in the final area; can you please give a bit more of a clue to which location you mean with pipes?