Best advice I can offer at this point is to grit your teeth and do it the hard way, within the raw ship.txt file. If the editor isn't cooperating, there's no point in relying on it (convenient as it might seem at first).
The room layouts aren't actually
difficult to get right, they're just tedious and it's easy to get lost in the mess of numbers.
You'll find a guide
here on how rooms and doors are set up. Note that any door that functions as an airlock
must be set up such that the first room number is whichever room ID has the door attached, and the second number is -1 (empty space). Reversing this order causes the game to crash.
Since it's easy to get confused and just throw your hands up, my suggestion would be to lay out everything as you want it in the ship editor,
take a screenshot of that layout, and use it as a visual guide while writing out your ship.txt. That way you can place numbers on the image to help keep room ID's and door numbers straight, black out the bits you've completed, and so forth. I won't lie and say it'll be tons of fun to do, but the joy of seeing your ship in game, functioning 100%, will vindicate everything you've worked for - and as with the game itself, make victory all the sweeter
