I actually did go with the bigger ship mod this time (or a blank map generated by one, anyway.) I'd say this one is maybe 2/3x bigger than my old one if you don't count the fucking tree, which I made when I was so stoned I don't even remember doing it, so it was kind of a surprise present from my past self the next day that causes massive lag. I originally drew a much larger outline but said nah, fuckit as I started filling things in. This time I started from the middle back and have just been expanding up and out from there. It'll be a perpetual work in progress, though it's already starting to look like end boss Kefka's pile of random bullshit.
So yeah, totally have that problem with building games. You should see my minecraft world I've been playing on since alpha. My solution is to go for builds where I can just keep glomming crap onto the sides and it'll always look pretty much finished in any state. So glad I didn't go for the "ship in a bottle ship" I originally started out on, though there's nothing to stop me from building a sideways bottle around this thing and half filling it with water some time. Looking forward to seeing what you've come up with.